Since my iPad (also iOS 6.0.1) works fine with my rt-n66u (and always has through every firmware I've used since April when I got it), not quite sure where to start. You didn't mention what firmware version you're using, or give any information about your settings, what procedure you use when you upgrade firmware, or other missing details (like which band are you using, 2.4 or 5GHz, security setup, how much wireless congestion there is in your area, etc.). It could even have to do with client devices interacting in some way on your router.
Can you please give more information about these things, there's a million possibilities of what could be happening. Like I said, the firmware has been solid for me and my iPad, so there's very likely other things going on.
Last edited by RogerSC; 11-16-2012 at 03:20 AM.