I also suspect that the new 2013 Nexus 7 has a design mistake that the gps antenna is too close to the wake/sleep sensor so the metal clips in cases with wake/sleep magnets block some of the gps signal. None of the cases sold by Asus have wake/sleep functionality, and since Asus knows better than anyone else where all the internals are located, that is a good indication that cases with wake/sleep cause some sort of problem.
I find this a very interesting observation. My GPS on my 2013 Nexus 7 is also toast, and I swear it was working when I first got the tablet about a month ago. I'm running the latest 4.3 with all updates. I also have a magnetic case and I noticed it really screwed with the compass but I didn't think that it would affect the GPS -- but I guess it does make sense. In any case, I bought mine online and I am NOT looking forward to going through Asus to get this replaced under warranty. I have tried everything -- factory resets, removing the case, going outside... The only way I can get a blip on google maps is with aGPS enabled, and I can tell it's not locking on any satellites because I'm only getting an approximate location. If I disable aGPS, google maps can't find me.