Hi Heath, As a first step can you please update to the latest version - there’s been a lot of bug fixes and enhancements in the last 500 or so builds https://www.finalbuilder.com/download.aspx
In the mean time I’ll try and replicate your problem with the latest build.
I'm now running the latest build (7.0.0.1065). I seem to have an issue with the 'check for updates' functionality which didn't tell me about the new release. One for another thread.
If you have a fix for the FTP upload issue for me to test let me know.