The id that is on the right-hand side of Settings > Store is the iTunes account that is currently logged in on the iPad - by tapping on it you should be able to log out of it and then be able to log in with a different account.
Is the id that is appearing in the App Store a previous account that you've used, or have you ever connected the iPad to somebody else's computer/account ?
I have the same problem as Mehrdad Erfani.
At times creating itunes account (for internationals) the Apple ID wasn't required or even available. All the purchase was done throughout itunes account.
Yesterday I wasn't able to update some applications as the ipad kept asking for Apple ID, PW etc which practically never existed. So I had to create an Apple ID. I thought if I'd created the Apple ID with the the exact same mail address as itunes, it would work. Disaster... I can by new application throughout the Apple ID. However my previous purchased applications cannot be updated, ipad assumes that it was purchased by a different account. If somehow I have to restructure the ipad, apperantly all the applications will be lost.
Over the years I have been struggling not to change to Android, as I had a huge investment into apple platform applications. For that reason I kept buying the whole iphone series upto iphone 5 and the whole ipad series upto ipad3... Somehow I felt like a kind of return of investment of the applications. Sadly I follow all the forums on this subject... Apperantly it was a problem for months... I believe it will be a big goodby to Apple world...