I've also had the same problems with the USB transfer. It happened on 3 different machines and on Win98 as well as on Win2000. It looks like the software is timing out somewhere in between. In Beta 7b or even in Beta 8 there was more debug output on the serial while transfering via USB. It said something like "preparing..." and then nothing happened for minutes, and then again the same "preparing...". I have had the same problems with Beta 8a, but it doesn't give the debug output anymore, so I can't give you the exact text that was appearing on the serial.
All over this explains the poor transfer rate via USB.

Felix