I recently built a system with an Intel I5 2500K processor. I made the goofy mistake of not perfectly securing the stock heat sink onto the processor. One of the clips wasn't quite all the way in, so the heat sink wasn't mounted flush onto the surface of the CPU. I've built plenty of systems, and I just got a little careless with this one.
I installed Win7 Ultimate, downloaded Sandra and 3DMark, and went to work testing things out. I noticed in Sandra that my benchmark scores were drastically underperforming the reference system with the same specs. When I ran 3DMark using the focused CPU tests, I noticed that the performance was clearly slowing midway through the test. This immediately led me to suspect heat issues. Sure enough, the CPU heat sink was scorching hot. I reseated the heat sink, and monitored the CPU temp during benchmarks. Happily, it was staying well within a comfortable range.
However, my benchmarks are still coming in a little lower than the reference. Both 3D Mark and Sandra put my CPU performance at 85% of the identical reference system. It's not too alarming at this point, but I'm curious if it's possible that the toasty conditions my CPU experienced as a result of my negligence damaged it so that it's not performing up to its specification.