Here's the latest beta of RealTemp with a few more minor features for Core i7 owners.
http://www.fileden.com/files/2008/3/3/1794507/RealTempBeta.zip
I just found a MS bug the other day when using XP that could lead to cores not being reported correctly. I'm glad you found your problem and I'm especially glad it wasn't a RealTemp issue.
CPU-Z should correctly report 4 cores and 8 threads when you have hyper threading enabled on a Core i7 so if anyone else looses a few cores, give that program a try too and see what it says.
In your screen shot, the APIC ID is reported as 0123 which means that you had hyper threading enabled and it was finding your first 4 threads. You should be seeing 01234567 now in that box in the Settings window. Your threads are not always in that order but most of the time on most motherboards they are. The pattern 02461357 is also common.
In the Boot window, this box is generally unchecked so the OS can find all of your cores.
http://img143.imageshack.us/img143/8269/boot.png
It's more of a debugging feature in case you have some software that doesn't play nice with multiple cores.