Well not 100% how these cpu id progs get their information. If they go through windows calls it could be a misreporting issue. Was going to say check control panel/system etc for multiprocessor but since you report 2 that part sounds ok.
Wonder if it is worth just resetting the BIOS back to default, just in case it has disabled two cores somewhere in there.
On the overclocking front, I'd tend to stick with stock voltage and increase in smaller chunks. There's plenty of info about, but obviously not your most urgent problem at the moment.
Good luck and hope you get a positive outcome.
Karl