well to answer you question...
a duo core 2 quad like a Q9400 cpu is a 4 core/4thread cpu. yes
I would reset the bios before reinstalling windows.
then boot in bios to ensure the cpu you installed is properly identified first (i.e. if it isn't windows will not identify it any better)
do that and report back, if still a problem please give use make and model of motherboard and cpu please.