Yes having the option for setting Active Directory user/pass as part of the folder config would be very useful. Storing the obfuscated credentials in a config file would not be desireable but if they pass compliance standards then that's all that matters. The issue we're trying to solve is login to the FTP site with non-Windows user/pass (versus Active Directory user/pass) and upload a file to a network share. However we don't want to give the CompleteFTP service acct permissions to the network share because that too would be exploitable considering the mutitude of network shares it would be granted.
BTW we are not yet customers and are evaluating the software. I am impressed with the quick, expert response to requests for features and forum posts.