The fact that your computer was complaining about keyboard not found, indicates to me something very strange is going wrong with your motherboard and BIOS, something that's unrelated to the empeg or to the serial cable.

Plugging something into the serial port should have absolutely no effect on the keyboard, and should not be related to anything plugged into the USB ports.

To answer your first question about the 2.0 software not working with USB, please read this.

In any case, if your empeg is successfully running 2.0 beta 13, that's actually just fine and is not much different from 2.0 final. What you need is to get the 2.0 version of Emplode from the www.empeg.com web site and then do the USB fix.

Should work fine after that, in theory.