I am having the same problem, but it happens anytime the unit is level (like on a desk) and I am not holding it, I can put the unit on ALL types of materials (i.e. paper pad, mouse pad, laminated desk, glass) and the top portion of the screen becomes unresponsive. I can't get notifications to work and the top 1/2" of the display is intermittent.
I found out the problem. This is really crazy but the evo is more touch sensitive on the bottom of its screen then top. Its not really noticeable without a skin, but with a skin its noticeable esp invisible shield. Stay away from invisible shields. They make the screen have a rubberized feeling that causes your finger to drag across the screen which causes the screen to have issues on the upper half of the evos display. I switched to sprints and its responds a lot better. Registers my fingers a lot better due to no drag. I also recommend phantom skins. The only reason I can think of for the evo having this issue is that the key board area needs more sensitivity than the rest of the phone. Maybe htc will fix this issue with an update.
Weren't there reports of the incredible having a similar issue in some cases?
I own an iPhone 1G, iPod Touch 2g and a iPhone 3Gs all have capacitive screens and none of them have this problems and all three of them have screen protectors on them.