Reading the instructions that came with my arctic silver order, it mentions that the thermal paste will not reach it's final "set" until several cycles of on and off (heat and relative cool) periods, have been completed.
In your case, I suspect there was an air bubble or other thermal defect, which the grease or paste, has since worked out.Thus improving it's thermal performance, and evening out the temps of your two cores.
If you think that's wild, here's a corker for ya. I bought a new Samsung Synchmaster 19" led monitor a few months back. Unfortunately, it had TWO defective LED's. Both showed bright red against any black or green background.
Now, it's been 3 months, and SOMEHOW in the last month and a half, first one, and now both of the bad led's, have returned to perfect service!
It's not like I'd miss them, especially with the black background of this forum.
Strange, but true, and I have no theory about why or how that could happen.
But I'm NOT complaining!
Adak