I noted something earlier while working on a track: all the audio I have running through UAD plugins are now phase flipped. Toggling back and forth makes this easier to hear.
Anyone else?

There's known problems with UAD plugs in X3.  http://forum.cakewalk.com/UAD2-problems-with-X3-Studio-m2898191.aspx 
 
I don't know if the phasing problem is related, but everything worked fin in X2a.  CW's on it.

Hey soundsubs,
 
I use a lot of UAD plugs so this thread got me intrigued. So in X3a I did the following:
 
1. I created two tracks of identical audio.
2. Reversed one phase.
3. Played the two tracks - nulled.
4. Returned phase.
5. Played both tracks - sounded normal.
6. Inserted (one at time) multiple UAD plugs on one track. Played both tracks - sounded normal.
6a. UAD Helios has a preset called flip the phase. If I play both tracks in phase but set the "flip the phase" preset on one track - nullled. 
 
IMO in X3a UAD plugs are NOT causing a track to go out of phase. Unless I'm missing something that you did.