Hey JD,
If you hide the toolbar (my default use) and make a FTP window the full height of the screen, then show the toolbar, it pushes the bottom of the FTP window off the bottom of the screen without anyway to re-fit it (even after re-starting Yummy as it remembers window position).
A very minor edge-case but I had shown the toolbar on a different FTP window and couldn't figure out why my status bar was gone a few days later on a different FTP server.
If you show the toolbar, can you check the height of the window/display and subtract that from the window height?
Cheers!
Jace