With Windows Desktop Search (I'm running 3.01) you cannot (by default) index you email if it is not configured to run in cached mode.
Well, you can change this through a group policy modification or thru this registry mod:
Create a DWORD registry key in:
called “PreventIndexingUncachedExchangeFolders” and setting it to a value of 0.
That's all. I tried both ways, and both worked.