Or the copper's base sucks as all TR bases. Have you checked the flatness of the cooler's base before mounting it?
Example of a True copper base:
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Intel Core 2 Duo E8400 E0 + Prolimatech Mega Shadow

DFI LanParty DK P45 T2RS Plus
Kingston HyperX 4GB DDR2 Low-Latency Kit
HIS ATi HD4870 512MB
1.6 TB HDD space
Xigmatek 650W Modular
Lian Li Armorsuit