i have a similar problem but i find that the middle part of my ipad screen is not responsive.
It first came to my attention when I was on the main screen and trying to reposition certain apps by dragging them across the middle of the screen. Apps on the right of the screen do not drag easy/at-all across the middle part to the left of the screen and vice-versa.
The same has happened in games and apps, for instance Words with Friends there are certain places I just cannot drag a tile to.
When I was using iAnnotatePDF and mucking around with the drawing tool testing this, I couldn't draw a circle (broke in the middle) and couldnt draw a line through that difficult area.
For some of the time I am lucky enough to be able to switch to portrait (or landscape) and reposition the material on the screen so that I am clicking in a different part and avoiding the middle of the screen, but the problem is becoming annoying.
Ive noticed the issue since i first got my ipad2, and before I placed a plastic protector on it. Does anyone else have problems with their middle part of the screen or is it just me?