Nearly killed PS2, swapmagic help?

Ok, I finnaly bought swapmagic 3.6 in order to load up my homebrew. Anyhoo, to test out the slidecard I stuck it into the PS2 and pulled out the tray. I was a little clumsy though as the tray came out crooked. I opened it up, fixed the tray and turned it on and "disc read error" popped up. After about an hour I recalibrated the laser and while my fat PS2 was still dismantled I loaded u swapmagic and then the snes emu. It worked!.

However, the DVD cd bundled along with my swapmagic pack only works when the PS2 is open. I'm totally and utterly confused. One second it's working when it's open the next think it can't even load up the disc when it's closed.

Any help?