I'm not a total newb, but this might just be one of those basic things that I am missing in a setting somewhere or a routing issue of some kind... 
 
Every track in sonar recorded or not, seems to have phase issues. I recently discovered that using the phase plugin from sonitus on all of my tracks has GREATLY improved my sound. Can anyone tell me why all of my tracks might be phased all the way one direction or another??
 
A little about my setup: 
 
I use a Mackie ProFX 16 and I run out of the sub 1&2 into the VS-100 3-4 inputs.  

first off, we need to know how you recorded each instruemtn/vocal. when you used 2 mic's, did you check for Phase?? When ever you use 2 or more microphones, you need to check for phase.
 
There is also a reverse phase button on each track, did you enable it by accident? 
 
CJ

That's the puzzling thing... most of these were done one instrument or voice with one condencser mic. When I play the tracks, it shows the phase as being completely right or left (I can't recall which right now) .. When I play more than one track together, regardless of panning the phase meter shows almost a mono correlation spectrum until I adjust the phase. 

.

.

the interleaves are mostly mono. The Monitor that shows me the phase correlation is on the master bus which is stereo. 
 
Typically, I will just plug a microphone into the mixer and then route that channel to the sub 1 & 2 pair out which goes into the VS100 Left 3/4 in Sonar.

.

I appreciate that, Mike. I have a feeling it's going to be something ridiculous. :)
I have nothing between the track and the bus. I discovered this totally raw. I don't have my machine in front of me right now.. I was hoping someone could just say something like "Yeah dummy... you have to route your blah blah to the whoosywhatsis" 

mancelot
When I play more than one track together, regardless of panning the phase meter shows almost a mono correlation spectrum until I adjust the phase.

I'm not sure what this means. Are you saying that two mono signals recorded at different times show a high correlation? They should be pretty much uncorrelated, even if they're the same part played on the same instrument. As such, different frequency components will go in and out of phase pretty much at random, and should not be particularly audible except maybe in the low bass region where you probably want to avoid mixing similar signals, especially if they're not panned hard left and right.
 
I'm not super-knowledgeable in this area, but I'd like to understand the problem better, and whether it's really an audible issue or just a spectral analysis phenomenon, and maybe a characteristic of the particular way in which the Sonitus plug-in derives and displays the information.
 
 
 
 

mancelot
 
Typically, I will just plug a microphone into the mixer and then route that channel to the sub 1 & 2 pair out which goes into the VS100 Left 3/4 in Sonar.

Does this mean you're taking your mono mic input and feeding the VS100 both left and right signals?   If so, I'd expect one of those to be "empty" and display as a one-sided stereo waveform.