OK solved this. Was further confused by device manager correctly reporting 12 CPUs so disagreeing with task manager and CoreTemp,.
Going to msconfig->Boot->Advanced Options there is a checkbox for 'number of processors' which was set to 6. Unticking the checkbox and rebooting fixes the issue...
Checked in the BIOS and it is set to ALL cores - tried setting to 5 but CoreTemp still reports 3 cores and task manager still only shows 6 threads. Can't see any power settings that would cause this and there weren't any issues when originally built.
adi - thanks for the suggestion, broke out...
Just over a year ago I built a rig using an Asus P6X58D-E motherboard and i7 970 (Gulftown) processor with W7-64 bit Installed. Hyper threading all enabled such that back then task manager showed 12 threads as expected and CoreTemp reported and showed temps for 6 cores. Now however I only seem...