I've discovered a bug where if the Audio compression is set to AAC, it is not possible to modify the Sample Rate. After playing around I found that if I change the compression back to PCM - alter the sample rate (e.g. from 44.1kHz to 48kHz) then switch back to AAC compression, it retains the new sample rate.
This is really weird and I can reproduce it intermittently, it varies depending on whether I'm using the inspector pane, (a random number of options appears) or the quicktime settings pop up window (settings are randomly greyed out).
It also happens with MPEG-4. (but not with PCM or apple lossless)