In order to test the new NativeProcess API of Air 2, I checked the required profile of "Extended Desktop" in my Publish Settings in CS5. When testing, though, I found NativeProcess was not supported in the debugger. I then published the FLA as a Windows EXE and installed it, and NativeProcess was working as expected. Having to publish a new exe every time I test is a big waste of time, so I instead used the command line ADL tool to debug, and by specifying "-profile extendedDesktop", I was now able to test my app with NativeProcess.
This should get fixed, as it is definitely an issue with the debugger running via Flash CS5.