:censored:? Lapped my heatsink, now running HOTTER!

Ok, I lapped the heatsink to a nice shiny mirror finish.  Looks great. 
I removed most of the metal that comprises the second hard disk cage.
I also reversed the smaller fan on the heatsink.  I couldn't reverse both of them due to not having the machine screws.
Now, my system is running about 2-5 degrees HOTTER than it was before I did all this?  What the hell?  Is it possible I didn't use enough Arctic Silver?
Matt

It might be shiny, but is it FLAT?
Or more precisely, is the surface exactly the same shape as the CPU (to atomic level)? I guess the most practical way to ensure this is to make both surfaces perfectly flat. The reason we use thermal paste is to fill in the microscopic gaps between the two metal surfaces - the trick is to use just enough to exactly fill in the gaps, without having any extra thickness. I'm told that a credit card is a good applicator! (I've also heard that toothpaste works remarkably well, until it dries out after a few minutes).
Oh, and you did run the tests at roughly the same ambient temperature, didn't you?
Cheers

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