I've been getting weird temps on my CPU too. I can't check them right now, because my PSU won't provide enough power to my GPU, but they were idling at 40, even on stock clocks. Since I have the E8400, and you have the QX9650, and they are both 45nm, this might be a problem with some 45nm chips.
It's not unusual to get different temperatures between cores on a quad-core, especially between core 0/1 and core 2/3. This is because of the chips' construction, which is basically two dual-cores placed side-by-side.
Even with a perfect mount, it's still easy to get differences, as the thermal material between the cores and the underside of IHS can vary, and there's really nothing you can do about that. Personally, a 6 degree difference at load is nothing to worry about.
i7 2600K | ASUS Maximus IV GENE-Z | GTX Titan | Corsair DDR3-2133
If your eqipment has not been really stressed or physically damaged in any way....
As a suggestion,If you are running XP Pro, go to task manager, right click on each process and set the affinity to cores 3 and 4 on half the background programs you are running all the time. This should reduce the temperature spread difference bettween the core pairs. Experiment with the higher cpu load programs and let them run for 10 mins or so before deciding . Keep your gaming programs on 4 cores, chat windows and VON programs can easily be ran by a single core. There are programs available that allows you to set the default core assignments on most processes, Run First is one of them. Some windows processes are not adjustable. I have noticed the 1st core pair is generally the hottest. TAT is the tool that works the individual core pairs seperately so you can really see the differences.