I'm replying just to let you know that someone read your post and I wish I could help you, but I have not had any problems at all with Direct FPT. If I would take a guess I would say it's some sort of settings issue.

The ftp server can disconnect you as well, it may have a session timeout itself.

Not uploading certain files could be a large host of things.
Definately get as much information about the settings (file size limit/permissions/size/etc) on the directories you're uploading to. What sort of connection are you working on? (I assume not dialup).