Have you checked you're vrm chipps if they are the same hight? And if the waterblock has a hight difference where the vrm chipps are??
When i mounted the block with level vrms and difference in block, i put on the thermal pad that is inn the instructions and then added an extra thin one where the hight difference was on the block.

I mounted first with just one pad and there was imprint on only the one side. So i added a thin one on the other side and put it back on.
I'm planing on putting on new thermal paste soon, then i'll check both my blocks and pads.