Is this an auto-run V/I job ran from a BAT file or shortcut? If so, short answer is No it won't run if all licenses in use. It like other ""Mas 90 style"" tasks run outside the Launcher (e.g. Timecard Punch-In Punch-Out, any BOI app/script) require an available license. Releases license when done but if job gets hung-up, license stays in use.
I like Core FTP Pro. It can schedule, encrypt, send emails when done, do scripted actions, support secure FTP (like FTP-S), has retry mechanisms, etc. A medical client uses it for HIPAA compliance. @NicoleRonchetti 's Star Trek FTP Voyager is is pretty cool too.