After looking at ED's inside GP2X pictures I noticed something. It appears that there are two big blobs of solder that look to be touching other components. If there is a short here it may be causing it to not work. Could this be the problem with these? I would imagine some of the others have this solder problem too.
Looking at the picture it doesn't look like the components that are being touched with the USB connector are actually receiving enough current (in any) to cause interference. After all, they're basically grounded to the connector, not the wires inside. And looking at a few USB connectors here it seems the resistance is enough to prevent any harm or data jumps.
If it works on one OS reliably and not on another, then its all software.