I believe I have the exact same problem as rsbitting above. Never believing the Nightstand app might be the issue, here's what I went through until I started suspecting the Nightstand app...
- Missed alarms every other day due to no sound starting right after iOS6 upgrade
- Restore to factory condition and my last backup - no change
- Took faulty iPad3 into my local Apple store while it was exhibiting no sound - they were miffed
- Got a replacement iPad3 restored from my last backup - still had problems missing alarms
- Restored to factory condition as new - no 3rd party apps
- Using built in clock app, I haven't missed an alarm in a couple of weeks
Of course, all of this has been over the period of Sept-Dec.
There may be more than one issue with sound disappearing on your iPad (and they might all be related to the same bug), but if you are using Nightstand, I believe that is certainly one of them.
I sent an email to the developer of Nightstand although I notice the app has not been updated for over a year so who knows if he even supports it any more.