If you're talking about whether the P4's IHS is flat or not, no, it shouldn't be an issue. It's my understanding that the IHS is actually fairly thin and flattens out when the correct pressure is applied by your cooling solution. I read that it was designed to do this by Intel's engineers, so the fact is it isn't expected to be perfectly flat prior to installation. I read through the other thread, don't know if other people are aware of the IHS design (as I described), but find it likely people's opinions on this may vary.
When it comes to your particular situation, I think it's very possible you're just not getting adequate pressure of the waterblock contacting the core.