I have noticed this also. If the audio is rolling before the video, it will often make a complex clip (i.e. synchronized clip) at 720p.
However, once the clip is in a sequence (project or compound clip) all the resolution in the clip is used. But what is lost is the ability to have the spacial conform settings be changed. It will always be on "fit". A bug or a result of a complex clip I believe. Compound Clips don't have the issue. . Better to put your synced clip in a compound clip, and break it apart inside there. Of course you have to do that at the get go.