Hopefully, some competent soul will have some idea what the [content edited] you're talking about and help you out.
In the meantime...
If I understand correctly, both the optimizer and CPU (Cool 'n' Quiet) driver "mess" with timing at a fairly low level. Have you tried running without either? What other hardware is installed? Post the rest of the system specs to give that competent soul an idea of what else may be involved.
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939Dual-SATA2 v1.05, BIOS v2.31
Opteron 165 (CCBWE 0550UPMW) @2.7GHz, 1.35V
TWINX2048-3200C2PT 2.5-3-3-6 1T
Thermaltake Big Typhoon
ATI X1800GTO