kbuihner:
Can you give us a little more information? Type of machine, what OS are you running, some basic info?
If I am reading this right, when you wake up your machine the screen has been "covered" and in order to find your way around, your cursor acts like an eraser and "uncovers' your background? Kind of like wiping condensation off a window or erasing a blackboard?
If that is what is happening to you, I had the same thing happen to my MacBook Air a month after I purchased it. My local Apple store couldn't figure it out either. It wasn't a major deal, I'd just have to 'erase' enough so I could find my log in window to type in my password and the machine would run just fine after that.
If I remember correctly, I was running Lion at the time. When I upgraded to Mountain Lion, that problem disappeared and I haven't seen it since. It must be "something" in Lion that does that.
If you are running Lion, I'd suggest an upgrade, or better yet, a clean install of another OS if your machine can handle it.
Or read CebuCity's suggestions in a post or two above yours and try that.
Good luck.
Pat