Yes, you are missing something here. Memtest only tests the memory, nothing else. Running Prime95 with small fft's only tests the cpu, nothing else. You
were aware that there are more than 2 parts to your computer system, weren't you?

If you run large fft's, it stresses the entire computer, besides of course the hd's and optical drives. Your chipset, for instance, hasn't played a part in either of the 2 tests you've run so far, yet it has as much to do with your system's stability as either of the 2 parts you've tested.