Did you try the Bio from MSI site instead? Or did you just see it happen with the original Fujitsu bio? The bio from MSI can be found at MSI Bio I got the 4000+ from the newegg at well (but haven't yet install it) so I would be very interested in knowning if you only saw that happen with the Fujitsu bio shipped with the board.
I flashed to the 7125NF1M-110-OEM BIOS mentioned above but it didn't solve my problem. (missing 1T/2T setting) I'm pretty sure the MSI BIOS (W7125NCG.1C0) will solve the problem but I'm waiting to here back from the MSI expert on the issue -- Syar2003 before I flash again.
These San Diego E6 chips are really Toledo X2's with one core disabled or damaged during fabrication. So what you have is a single core chip on a very large die. It's stock voltage is very low (1.35v) and runs EXTREMELY cool. I had the clock speed stable at 2900 under Prime stress and temps only got up to 47c max. (Arctic 64 cooler)
Your Newegg 4000+ will almost certainly have the E6 stepping so keep an eye out for the missing command rate settings. I'll report back soon on whether the other BIOS solves this problem or not.