I just had exaclty the same problem with Adobe CS3 on my Win7-64-bit system that Quicktime work properly as stand alone application, but the Adobe CS3 media encoder will not show the AAC option!
I spent about a complete day to find the very simple solution:
As Quicktime is still a 32-bit Application you need to install Quicktime in WinXP-SR2 compatible mode to make AAC show up and working in Adobe Premiere CS3 media encoder!!!
Hope this help someone wasting time … !?