You can set it manually to 100Mhz in bios. I think it runs at that value on auto anyway. AMD Overdrive always gave me strange readings, so I gave up on it. Unless you're experiencing some problems indicating that the PCI freq. is higher than 100Mhz I wouldn't worry.
A good deal of the problems listed here is common, at least within Gigabyte boards. The 1.6v RAM voltage instead of 1.5v I can't figure out. I have this problem on my other MB but on my GA-790XTA-UD4 it works as it should. HT link and bus speed are likely both read properly if they're only a little higher than auto ( 200Mhz/2000Mhz ). For some reason bus speed is actually running 200.8/200.9Mhz which equals a higher HT link.
edit: I downloaded AOD again just to see what it'd show me. Good thing I wasn't drinking anything or I'd be cleaning my screen now
. Somehow, I seriously doubt that my PCIe is running at 345Mhz. The GPU going crazy aside, I think I'd have to increase PCIe volts to even dream of such values. Not to mention RAM volts reported as 1.6 when it's over 1.7v in reality.
What can I say... AOD sucks and is probably potentially dangerous.