I believe the issue is too many pages of apps.
This happened to my iPad after updating to IOS 5. The problem seemed to be that it downloaded ALL apps to my iPad, not just what I previously had on my iPad. Meaning, it took apps from my iPhone, my husband's iPhone, and added them to the iPad. This resulted in too many pages of apps. I moved them into folders and deleted some. This decreased the number of pages, and so I thought all was fine. Then the next day when I went to use an app that I knew was on there, I couldn't find the icon. Yet, if I did a search, the app was there "somewhere". All I had to do was a hard shut down on the iPad and I rebooted it and they came back. I had to do some more folder condensing, and have been fine ever since.