What would be the reason for my MacBook Pro to not close?
My MacBook Pro will not close shut all the way..I'm guessing there is something wrong with the magnets..
2.2, 2.4, 2.5, or 2.6 GHz Core 2 Duo processor
or bent/broken latch using this guide MacBook Pro 15" Core 2 Duo Models A1226 and A1260 Rear Display Bezel Replacement you could dismantle the rear display case to the point of identifying any misaligned parts or wires, bent or broken latches, and take appropriate repair action.
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Your top and bottom cases may be out of alignment. When you say "that it will not shut all the way, I assume you mean that it will not latch. There are two latches in the top and the receptacles are in the bottom with the magnets. Carefully close the lid and see if they line up and see if the top latches are being pulled down. Gently push the top case in the direction it needs to go after observations. You can also inspect the hooks to see if they are broken or bent.
This isn't always the result of misalignment. That button stops coming back out all the way over time, even if there's no dust or crud in there. I've blown the thing out at 150 PSI and cleaned it as best as I could, it just gets old.
Do this and you'll fix it every time. This has had a 100% success rate over the past five years, with no customers ever coming back.