I'm getting the same exact error too, and like you I've loaded and unloaded the Zune software enough (and from enough different sources and in enough different versions) to be fairly sure that it's not the Zune software. I've made sure my USB drivers are up to date, as well as everything else on my machine. Also, my Zune charges on the USB cord, and plays just fine on it's own, so again, I'm fairly sure it's not the Zune. (I would try it on my work machine, but alas, I'm still at Windows 2000 here. :)
The outside info I've seen about this (such as this link
here) has suggested that the message is really reporting a conflict in USB drivers. Specific examples I've seen mentioned are a PS3 driver and a CVS digital camera hack. I found them through searching the phrase '"The system cannot find the file specified" zune' At this point, though, I know I haven't used those drivers, and I can't figure out how to track down other possible drivers.