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They are entirely different chips. The socket 939 Athlon 64's have a different pin structure that allows the clock speed and L2 cache to be lowered without a performance loss. Most of the socket 754 Athlon 64's have 1 MB of L2 cache while the 939's usually have 512kb even though they perform the same. In some tests, the 939's actually perform better due to a more efficient memory interface. In short, yes, they're supposed to be different.
-Lasereth
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"A Darwinian attacks his theory, seeking to find flaws. An ID believer defends his theory, seeking to conceal flaws." -Roger Ebert
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