Randallizer: If you look at CPU-Z it shows that you have only 2 cores and 4 threads. That's the reason why RealTemp is only showing temperature information for two of your cores. With a Core i7 it should show either 4 cores and 4 threads or if you have hyper threading enabled in the bios then it should show 4 cores and 8 threads.
You have a problem with your bios or how you have Windows set up. If your bios is set up correctly then try running msconfig and have a look in the Advanced Boot options.
Usually you don't have to mess with that but you could try forcing it to the largest number of cores available.
The 0123 for APIC ID in the RealTemp Settings window shows it is only seeing 4 threads. Did you do a fresh install of Vista when you built this computer?
File_1993: All 45nm Core 2 sensors are not great at reporting accurate temperatures. They weren't designed for this purpose and it shows.
What I've found in my testing is that TJMax is not a fixed number. It's not the same from one E8400 to another and the shocking part is that it isn't even consistent from one core to the next on the same CPU. Most of the 65nm Dual Core CPUs were pretty close from core to core but there are some 45nm sensors where the difference is 10C from core to core.
Try setting your idle calibration both back to 0.0 and 0.0.
Use TJMax = 100 / 107 for your two cores.
Now from idle to full load your cores should track each other very closely.
100 / 107 is my best guess on the data you've shown me. I took my Q6600 up into the 70C to 90+C range and there was a constant difference of 5C. I replaced the heat sink and the paste and etc. and finally concluded that TJMax is not consistent. For my Quad I use TJMax = 100 / 100 / 105 / 105.
Once you've set TJMax like this, try and run your CPU at low MHz and low core voltage and compare your results to your room temperature as outlined in the docs. The slopes of your two temperature curves are very similar. It's mostly just a difference in how TJMax is calibrated. Using the calibrated word on these sensors is kind of stretching it.