You are not alone. I tried all the fixes, multiple times, but nothing worked.
I think there's nothing to do but wait. The fact that many of us are experiencing the same problem with the iPad Remote app, and the fact that the iPhone Remote app still works fine, tells me it's a glitch in the software - maybe Apple TV 5.2, maybe iOS 6.1 (I updated to both yesterday).
Meanwhile, since Apple does not read these forums, I suggest we all leave comments on their feedback page: http://www.apple.com/feedback/appletv.html
That way they'll at least know a bunch of us are having this issue.
Hopefully Apple will issue a fix soon.
Ipad remote works fine now as of 30 minutes ago apple released a new update to it. I was having the same issues as everyone else. I was racking my brains. Thank you Apple for listening, that was a very fast fix and I think its working even better now. I'm running Ipad mini with ios 6.1 and ATV3 with the latest update to 5.2