Dude, you need to try a new processor. See if it does the same thing.
My guess, and I've seen the exact thing on several systems, is that the processor got overheated, and now is not up to the performance level it should be. Even though you've changed the heat-sync/fan the damage might already be done...
My guess, and I've seen the exact thing on several systems, is that the processor got overheated, and now is not up to the performance level it should be. Even though you've changed the heat-sync/fan the damage might already be done...