I'm posting the results of your suggested modification below in the hope it might help you diagnose the problem. However, note that bytesTransferred() is only called from the ProgressMonitor and the problem persists even without calling the ProgressMonitor.
I'm experiencing the problem with a variety of servers. The one I'm interfacing with here is a Linux web server.
run:
INFO [TestConcurrent] 15 May 2012 22:20:28.034 : Starting upload: /public_html/Curious/ftp/IMGP2704.DNG
DEBUG [FTPClient] 15 May 2012 22:20:28.050 : Class: com.enterprisedt.net.ftp.FTPClient
Location: file:/C:/Users/Curious/Documents/NetBeansProjects/DebugFTP/src/edtftpj.jar
Version: 2.3.0
Build timestamp: 26-Aug-2011 13:52:07 EST
Java version: 1.6.0_26
CLASSPATH: C:\Users\Curious\Documents\NetBeansProjects\DebugFTP\src\edtftpj.jar;C:\Users\Curious\Documents\NetBeansProjects\DebugFTP\build\classes;C:\Users\Curious\Documents\NetBeansProjects\DebugFTP\src
OS name: Windows Vista
OS arch: x86
OS version: 6.0
DEBUG [FTPClient] 15 May 2012 22:20:28.075 : Connecting to ftp.somename.com/67.20.76.108:21
INFO [TestConcurrent] 15 May 2012 22:20:28.235 : Starting upload: /public_html/Curious/ftp/IMGP2705.DNG
DEBUG [FTPClient] 15 May 2012 22:20:28.235 : Class: com.enterprisedt.net.ftp.FTPClient
Location: file:/C:/Users/Curious/Documents/NetBeansProjects/DebugFTP/src/edtftpj.jar
Version: 2.3.0
Build timestamp: 26-Aug-2011 13:52:07 EST
Java version: 1.6.0_26
CLASSPATH: C:\Users\Curious\Documents\NetBeansProjects\DebugFTP\src\edtftpj.jar;C:\Users\Curious\Documents\NetBeansProjects\DebugFTP\build\classes;C:\Users\Curious\Documents\NetBeansProjects\DebugFTP\src
OS name: Windows Vista
OS arch: x86
OS version: 6.0
DEBUG [FTPClient] 15 May 2012 22:20:28.235 : Connecting to ftp.somename.com/67.20.76.108:21
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.322 : 220---------- Welcome to Pure-FTPd [privsep] [TLS] ----------
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.322 : 220-You are user number 5 of 1000 allowed.
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.322 : 220-Local time is now 20:20. Server port: 21.
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.323 : 220-This is a private system - No anonymous login
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.323 : 220-IPv6 connections are also welcome on this server.
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.323 : 220 You will be disconnected after 15 minutes of inactivity.
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.324 : ---> USER somename
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.433 : 331 User somename OK. Password required
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.433 : ---> PASS ********
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.454 : 220---------- Welcome to Pure-FTPd [privsep] [TLS] ----------
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.454 : 220-You are user number 6 of 1000 allowed.
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.454 : 220-Local time is now 20:20. Server port: 21.
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.454 : 220-This is a private system - No anonymous login
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.455 : 220-IPv6 connections are also welcome on this server.
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.455 : 220 You will be disconnected after 15 minutes of inactivity.
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.455 : ---> USER somename
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.563 : 331 User somename OK. Password required
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.563 : ---> PASS ********
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.624 : 230 OK. Current restricted directory is /
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.624 : ---> PWD
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.732 : 257 "/" is your current location
DEBUG [FTPClient] 15 May 2012 22:20:28.732 : Attempt #1
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.733 : ---> PASV
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.757 : 230 OK. Current restricted directory is /
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.757 : ---> PWD
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.842 : 227 Entering Passive Mode (67,20,76,108,40,11)
INFO [FTPControlSocket] 15 May 2012 22:20:28.842 : Substituting server supplied IP (67.20.76.108) with remote host IP (67.20.76.108)
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.867 : 257 "/" is your current location
DEBUG [FTPClient] 15 May 2012 22:20:28.867 : Attempt #1
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.867 : ---> PASV
DEBUG [FTPControlSocket] 15 May 2012 22:20:28.975 : 227 Entering Passive Mode (67,20,76,108,237,251)
INFO [FTPControlSocket] 15 May 2012 22:20:28.975 : Substituting server supplied IP (67.20.76.108) with remote host IP (67.20.76.108)
DEBUG [FTPControlSocket] 15 May 2012 22:20:29.046 : ---> STOR /public_html/Curious/ftp/IMGP2704.DNG
DEBUG [FTPControlSocket] 15 May 2012 22:20:29.163 : 150 Accepted data connection
DEBUG [FTPControlSocket] 15 May 2012 22:20:29.179 : ---> STOR /public_html/Curious/ftp/IMGP2705.DNG
DEBUG [FTPControlSocket] 15 May 2012 22:20:29.295 : 150 Accepted data connection
INFO [ProgressMonitor] 15 May 2012 22:20:33.153 : /public_html/Curious/ftp/IMGP2704.DNG 3008390 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:20:33.153 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:20:38.153 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:20:41.708 : /public_html/Curious/ftp/IMGP2704.DNG 6017329 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:20:41.708 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:20:46.708 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:20:46.845 : /public_html/Curious/ftp/IMGP2705.DNG 3009643 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:20:46.845 : Sleeping for 5s
INFO [ProgressMonitor] 15 May 2012 22:20:50.059 : /public_html/Curious/ftp/IMGP2704.DNG 9027052 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:20:50.060 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:20:51.845 : Woke up
DEBUG [ProgressMonitor] 15 May 2012 22:20:55.060 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:20:58.409 : /public_html/Curious/ftp/IMGP2704.DNG 12036521 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:20:58.409 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:21:03.409 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:21:05.996 : /public_html/Curious/ftp/IMGP2705.DNG 6019788 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:21:05.996 : Sleeping for 5s
INFO [ProgressMonitor] 15 May 2012 22:21:07.031 : /public_html/Curious/ftp/IMGP2704.DNG 15046136 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:21:07.031 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:21:10.997 : Woke up
DEBUG [ProgressMonitor] 15 May 2012 22:21:12.031 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:21:15.890 : /public_html/Curious/ftp/IMGP2704.DNG 18055138 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:21:15.890 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:21:20.890 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:21:22.671 : /public_html/Curious/ftp/IMGP2705.DNG 9029854 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:21:22.671 : Sleeping for 5s
INFO [ProgressMonitor] 15 May 2012 22:21:24.377 : /public_html/Curious/ftp/IMGP2704.DNG 21063149 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:21:24.377 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:21:27.671 : Woke up
DEBUG [ProgressMonitor] 15 May 2012 22:21:29.377 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:21:32.729 : /public_html/Curious/ftp/IMGP2704.DNG 24015550 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:21:32.729 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:21:37.729 : Woke up
DEBUG [FTPClient] 15 May 2012 22:21:37.729 : Transferred 24015550 bytes to remote host
DEBUG [FTPControlSocket] 15 May 2012 22:21:37.729 : 226-File successfully transferred
DEBUG [FTPControlSocket] 15 May 2012 22:21:37.729 : 226 63.683 seconds (measured here), 367.08 Kbytes per second
DEBUG [FTPControlSocket] 15 May 2012 22:21:37.729 : ---> QUIT
DEBUG [FTPControlSocket] 15 May 2012 22:21:37.838 : 221-Goodbye. You uploaded 23377 and downloaded 0 kbytes.
DEBUG [FTPControlSocket] 15 May 2012 22:21:37.838 : 221 Logout.
INFO [TestConcurrent] 15 May 2012 22:21:37.839 : Finished upload: /public_html/Curious/ftp/IMGP2704.DNG
INFO [ProgressMonitor] 15 May 2012 22:21:42.522 : /public_html/Curious/ftp/IMGP2705.DNG 12040227 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:21:42.522 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:21:47.522 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:22:03.123 : /public_html/Curious/ftp/IMGP2705.DNG 15050171 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:22:03.124 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:22:08.124 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:22:26.947 : /public_html/Curious/ftp/IMGP2705.DNG 18059689 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:22:26.947 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:22:31.947 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:22:44.894 : /public_html/Curious/ftp/IMGP2705.DNG 21067692 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:22:44.895 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:22:49.895 : Woke up
INFO [ProgressMonitor] 15 May 2012 22:22:58.179 : /public_html/Curious/ftp/IMGP2705.DNG 22935622 bytes
DEBUG [ProgressMonitor] 15 May 2012 22:22:58.179 : Sleeping for 5s
DEBUG [ProgressMonitor] 15 May 2012 22:23:03.179 : Woke up
DEBUG [FTPClient] 15 May 2012 22:23:03.179 : Transferred 22935622 bytes to remote host
DEBUG [FTPControlSocket] 15 May 2012 22:23:03.179 : 226-File successfully transferred
DEBUG [FTPControlSocket] 15 May 2012 22:23:03.179 : 226 149.004 seconds (measured here), 149.80 Kbytes per second
DEBUG [FTPControlSocket] 15 May 2012 22:23:03.179 : ---> QUIT
DEBUG [FTPControlSocket] 15 May 2012 22:23:03.288 : 221-Goodbye. You uploaded 22321 and downloaded 0 kbytes.
DEBUG [FTPControlSocket] 15 May 2012 22:23:03.288 : 221 Logout.
INFO [TestConcurrent] 15 May 2012 22:23:03.288 : Finished upload: /public_html/Curious/ftp/IMGP2705.DNG
BUILD SUCCESSFUL (total time: 2 minutes 35 seconds)