Here is how Toms Hardware describes the difference.
"This correlation is evident particularly in the case of MSI. The manufacturer offers two versions of the MSI K7T Pro2. The classic K7T Pro2 has the ATA/66-Southbridge (VT82C686A), while the K7T Pro2-A is based on the ATA/100-Southbridge (VT82C686B). Apart from this difference, the boards are constructed identically. The result shown above reveals that the VT82C686B appears to slow down the Northbridge. A different graphics driver version from NVIDIA does not change this trend, either"
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