From your description, it seems to me that there is a fundamental problem with either your Internet connection or your server - maybe both.
While Yummy FTP is designed to be resilient to unreliable connections and servers, there is point at which it will still be unable to recover if the reliability of the connection/server is very bad.
Looking at my records I see that you purchased Yummy FTP back in February, so I assume that was working without any problems then? Otherwise I don't see any reason you would have bought it.
So, something has changed since then, and my first recommendation would be contact your Internet service provider and/or Web hosting provider to see what they have to say.
While you wait for their answer, you could try with the latest beta version to see if there is any difference:
http://www.yummysoftware.com/beta/latest/YummyFTP.dmgOne last thing to try: In some very rare cases, servers react badly to the use of multiple simultaneous connections that Yummy uses to speed up transfers. To eliminate this as a possibility try entering 1 into the Max Connections Per Server setting in the Transfers panel of the Preferences.
Out of interest, could you please repeat a failed upload of multiple files, then select Save FTP Transcript from the File menu and send me (support at yummysoftware dot com) the resulting file?