Well, this is certainly one of the more unusual issues I've ever seen in my two-decade computer troubleshooting career
You win a prize! Or something
I guess it comes back down to basic troubleshooting process of elimination. It's not the hardware of the ATV2 (it was replaced), not your network infrastructure (tried it on different routes w/different cables), so perhaps we need to look back at what's actually being done.
You said you're tarballing the XBMC folder. If you can copy the XBMC folder back and forth without any problems (you can, right?), but a tarball of the XBMC folder does NOT copy back and forth fine, then it might be a problem with the tarball process. Maybe an incorrect or unsupported parameter is being used, or something (I'm not familiar with tarballing per se, although I've heard of it of course).
What if you tarball something else on the ATV2 that reaches the same approximate file size, and try with that?
The only other thing I could suggest would be to find a friend, take the ATV2 to his house, hook it up to his network, and see if you can copy the tarball to his computer. Just to absolutely confirm it's nothing in your house/electrics/setup.
It just seems like this must be a solvable issue--there's no reason you should have to resort to using wireless for this purpose only and then wired for other purposes