erm... ok, where you doing this while the CPU was still VERY hot (or even turned on)?? but no, i highly doubt what you see is burned, its thermal paste, designed to get hot and get rid if heat fisat, i doubt it would burn. It will get hard, but all paste does that.
your CPU might have a small convexed top to it, and pushed the thermal paste to the sides and started to expose the processor a littlebit..... oooooor it could mean that your processor got SOOOO hot that it fried the thermal greese properties of it and left the silver...
the cpu is new, im buiding my pc.. i was intalling it for the first time, when i got to install the heatsink i guess i moved it a lil too much tryin to make the metal clips grab the sides, i went to look at it to see if it was still in place and i saw that the cpu had two differnt silver colors, just like it was to put acid on something. im just worried that it messed up my cpu, because i looked under the heatsink there was another type of paste (square shape) which came with it.