I think I had this phenomenon when I enabled a send to a bus during playback - eg. a snare drum goes to a bus both directly and via a compression bus. Starting with the send to compression off, then switching it on during playback, gave a phased sound on the final bus. Stopping and restarting transport fixed it. But this was a while ago. (Might have even been in 8.5 when I experienced it.)

I just confirmed my repro case above.
 
Set up 1 softsynth (in my case, Superior Drummer 2), 1 bus with Sonitus Compressor on it, and 1 master bus.
Softsynth sends to the compressor bus and outputs to the master bus. Compressor bus outputs to master bus.
Set the compressor up almost like a limiter so there isn't much effect on peak volume levels (as that will confuse matters),
Disable the send.
Start playback, ideally of a piece playing the same note over and over.
Enable the send, listen to how the sound changes to become phasey.

Do you still have the phasey sound if you disable the comp in the bus?
 

No, it's the compressor. I get the phasing if I enable the send to a bus with the compressor on it during playback, and if the send was already enabled but I switch the compressor on during playback.

FWIW I'm also doing some null testing with tracks and buses to see if I can find anything reproducible regarding phase issues if effects are not in the path.

I've had phasiness when sending tracks to a bus before. Sometimes it would happen after the first iteration of a loop, or when toggling loops on and off during playback. There are certain actions, like toggling loops or turning effects on and off during playback, which seem to cause Sonar to go out of whack time wise. I notice it a lot with time based effects which go out of sync when turning loops on or off. 
 
The send phasiness is something I've noticed when sending dry bass signal to a bus with an amp sim on it. After the first iteration of a loop, the bass would suddenly sound out of phase and stopping and starting was the only way to fix it. I haven't seen this for a while but I've certainly seen other instances of send phasiness. I have one going on right now, a vocal track which gets sent to a compression bus. Every now and then it will sound out of phase and I have to stop and start to fix it. 

Sharke, I'm seeing a pattern here...which compressor?
 
As to the other examples, can you recall whether this changed at all with X3e? Also, I'm not surprised that stopping and starting is a fix, it gives SONAR a chance to "re-align" things.
 
Could you do me a favor - next time this happens, instead of stopping and starting, toggle PDC and let me know what happens.

Craig, sorry I never responded to your question in this (fairly) old thread, it must have slipped through the net. I came back to it after having a really bad time with this problem tonight. The compressor I seem to have the most problem with when it comes to bus phasing is Native Instrument's VC76. It's a great compressor for doing NY compression but it just does not seem to play nicely on a bus. Sometimes the phasing is fixed by stopping and starting, other times it just won't go away until I close and relaunch the project. I've toggled PDC to no avail. 

I think there might be something to look into.
 
I ran Waves TrueVerb on an effects bus - and forgot to turn direct signal off on a preset - and got this odd distortion on master with Waves L2. Turning direct off - it went away.
 
Most noticable when reaching treshold of L2, almost like bitcrushed dist.
But never had anything like that before.
 
I am to investigate further on another daw and come back, if a Waves issue. But since I read this thread I put it here. TrueVerb is not to have any latency.

Interesting thread ...
 
I was aware of this phasing issues as regards adding sends while playback is running (and stop/start fixing it), but I still consider it a bit of a hazzle when it comes to switching sends to reverb/delay buses on and off (which BTW quite frequently causes the audio engine to stop) ... this should be investigated by Cakewalk to ensure this doesn't throw PDC out of sync and keeps the audio engine running at all times.
 
while the stop/start "workaround" had "fixed" the problem up to now, I have now run into a more mysterious situation where I get phasing even after start/stop when using AD2 as VSTi with a bus set up for NY compression, but not when using AD2 bounced to audio tracks in the same configuration ... really strange (more here: http://forum.cakewalk.com/FindPost/3193915)