current application goes in and out and I cannot complete a command

This problem has occurred in different applications-Photoshop, mail, etc. I will be in an app; I want to reply or send in mail; or do anything in Photoshop, and I can't. The screen has shrunk, I might have other small screens of apps show up; my command did not go through. If I click on my current app, it gets larger. I then try to do a command in the app and it shrinks again. This might have several times in concession. I generally have to leave the app of awhile. This only happens when I have been on the computer for about an hour or longer.

I have a MACPRO (eary 2009)