This seems to be all over the place. I documented this as the #1 problem in the Known Issues sticky.
Some files transferred fine (my Titanium Backup, for instance), but when I tried photos or movies, they would all time out. I searched for some explanation, and I found that it possibly had to do with permissions, so I was able to get a tiny bit of success by creating new folders. However, I'd still have random file transfer hangs. Acted like the device wasn't connected anymore.
My final solution was to use the cable that came with the Gnex. After that, everything has worked flawlessly. I had been using another USB-microUSB cable that I used with many other devices with no ill results. But for whatever reason, the cable that comes with the GNex is the only one that I can use reliably.
Yes, I know USB is supposed to be a standard, but perhaps there are crosstalk, emi, or other uber obscure issues (contact plating causing increased capacitance) that is causing the trouble.
But I can say for certainty that I can 100% replicate the issue between the old cable and then new one. Same computer with same USB port, different computers, etc. All with the same result.