ARENT YOU THE GUY FROM GBATEMP?! Try properly snapping on the back cover. There are various antennas and perhaps they weren't properly lined up. Don't really think removing a back cover will cause this, my 2 cents is that it just isn't properly snap shut.
EDIT: pretty sure you are. You owned an Xperia Play and we discussed it in a GBATemp thread before saying that android 4.1 was rolling out to Nexus devices. We also met in the Gin2JB thread.
I had this problem with nfc and wireless charging, turned out the back panel just wasn't set properly. I believe there are antennas that need to contact components on the motherboard. Try pushing a little harder all over the back until you hear it snap.
Sent from my Nexus 5
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