If your waterblock uses bolts through the card, I'd cut a piece of plexiglass that was just larger then the gpu and use longer bolts to bolt through the plexi>agp card>waterblock.
That should keep it nice and flat.
Firstly though, you should find the cause before building a band-aid for it. Is it that the block was too tight? Was a manufacturing defect? Is it....eek....getting wet? Are your hoses too heavy? Is your cases backplane tweaked or motherboard out of proper alignment?
(I try to install the vid card, and one pci card, then tighten the bolts to the motherboard, then remove the agp card to tighten the bolt underneath it).
You could also try loosening the bolts that hold the metal slot cover onto the card, then retightening it without removing it from the case. Sometimes those are installed crooked at the factory.
Whatever you do be gentle, you don't want to break it, eh? Luck to ya.