That compound you took off was MX5, Arctic Cooling's premier paste (I believe). Anyways, I'd take the heatsink back off, clean both the heatsink and the processor, get a picture (probably from google) of where the dies are located in reference to the integrated heat spreader (IHS), and drop two small drops of AS5 on about where the dies are located. You're probably right about a bad mounting.
In a dual-core system, one core will generally be hotter than the other, due to a higher workload, different positioning beneath the IHS, simply being a different chip, etc. It is nothing to worry about.
One core hotter than the other is normal, its the same situation with 2 GPUs in SLI because 1 of the GPUs is the primary and percentagewise it does more work.
This is to address the Artic Cooling Freezer 64, the base is smaller than the CPUs heatspreader, [at least on mine it is], and when clamped into position the clamp design would pull the base off center quite a bit. I adjusted the bend on the catch side so when the latch side was fully engaged it would sit squarely on the center of the CPU heatspreader.
You may want to take a good look at the positioning of the heatsink base in relation to the CPU heatspreader and see if yours is seating properly, Artic Cooling may have addressed this issue by now, but I seriously doubt it, IMO they should have made the base the same size or larger than the heatspreader.
I was also surprised that the Heatsink didn't completely cover the heatspreader! WTF?
Yeah that seems like a manufacturing design screwup, if its aligned dead center theres about 1/8'' of exposed CPU heatspreader all the way around, if it doesn't center properly theres as much as 1/4" of the heatspreader exposed on the latch side.
Believe it or not I took mine back off and got cooler running temps from the stock AMD CPU cooler using Artic Silver 5.
Well if it makes you feel better I not only have the Artic Cooling Freezer 64 on the shelf, but a pair of Accelero X1s also on the shelf, they didn't cool any better than the stock GPU coolers did and took up a massive amount of room to install.
Well, the Arctic Freezer is cooling off in its box on the shelf now, and the stock fan is in. My CPU temps still have the 10C differential, but they are BOTH 10C cooler than they were! And I don't think it's the FX-60 that is the trouble here, it is definitely the 8800gts. I have a theory that the g8 was warming the giant heatsink on the AC64 from it's pci-e slot. With the smaller stock sink and fan setup maybe the heat won't transfer over so easily.
Glad I bought that AC64 when it was $15 instead of $30, and NEVER AGAIN! Time to head over to NEgg and abuse it in a review.
Then I'll head to the "should I buy the e6600 or FX-60" thread and whatch the fireworks. God bless America!
Hey man, I have a freezer 64 pro and it killed a Opteron 175!!
That stupid heatsink pulls to one side of the cpu and over laps.
It cracked the core but luckinly AMD shipped me a brand new opty.
I emailed freezer pro's company and told them that this happend as a direct result of using the cooler.
They asked me explain what happened, but they never responded.
I WAS LUCKY AMD replaced the CPU, cause
arctic cooling wouldn't have done crap all.
PLUS the heatsink doesn't have a straight edge, it's bowed shape.