Yep, I had an old MIDI keyboard that would sporadically send all kinds of weird stuff into my sequencer, including pitch bend and aftertouch info - that could easily do things like change the pitch on your tracks. Definitely worth unplugging your controller just for troubleshooting.
 
Did you try bouncing down the offending file and seeing if it was still out of tune?
 
 

Thanks for all of your help.  I ended up just going for Platinum.  This was turning into a nightmare and I just don't have time for this crap. 

Did Platinum solve the issue?

No and I am beyond angry right now.  I called Cakewalk today about X2 (before I decided to get Platinum) and the tech guy says, "we don't support X2 anymore, but I'll send you some suggestions in your e-mail, you'll get it in five minutes."  Nothing.  Now, the same f'ing thing is happening and I have NO help. 
 
I guess I'm moving to Cubase if I don't figure this out.  Maybe they'll actually help me with their products.  I would hope....

For your midi tracks:   Do you ever intentionally change the pitch via transpose?  Do you ever change the pitch via pitch wheel?
 
If you do either of these thinking you've changed only one area and you have accidentally changed a much larger area, then that could be a culprit.   I've done both.   Sonar's selection is very peculiar in many situations ... you can easily have an actual selection that is completely different than what you think it is.   This happens to me for transpose, pitch change, velocity change, and length --- all at one time or another.

Check the pitch of the guitar audio file in another player. possibly there was a clocking problem while it was being recorded and the file header is saying it's 44.1 when the interface clock was actually running at 48.

If you're willing to upload a CWB of a small project that has the problem (to Dropbox or something like that), I'd be happy to take a quick look at it for you. 

You guys are awesome!  I'll reply to you all more directly later, I have to go to work.  One thing that might help:  when I open the standalone version of Rapture Session (was just testing out the pitch), the onscreen keyboard says it's the correct note, but it's not.  It's a whole step off.  So, I go into the edit function of the controller, make it go down two half steps so it's the right note, power the unit off, turn it back on, open Rapture again.... back to being the wrong note. 
 
Lord Tim, I'm going to take you up on that.... I'll be back later.  Thank you all once again!

Have you tried using the free MIDIOX utility (search goggle for their website) to see if your M-Audio Keystation is sending the correct MIDI codes? This utility has been very helpful for solving some of the MIDI gremlins I've had. 

There are so many reasons why this could be happening, but I'd bet none of them is due to something happening within SONAR. SONAR can only do what it's told to do. Something is feeding it bogus information. There's no guarantee another DAW would solve your problem.
 
I suggest borrowing a different interface and controller to see what happens. Also, if the controller has some sort of reset function, use that.
 
If the problem is outside of SONAR it's not surprising that support can't help. If it is inside of SONAR, it seems virtually impossible that no one else has experienced this problem.