Still at work, but just a quick reply....definitely going to reply more later. Yes, I kinda am leaning towards it not being Sonar. I did what M-Audio suggested as a reset.....it didn't work.

I second installing MidiOX and taking a look at what the MIDI data passing in and out of Sonar and the controller actually is. Spurious pitch-bend data might well cause the problem you're describing, and I've certainly come across keyboard controllers that didn't accurately centre their pitch wheels but would once in a while trickle out pitch-bend instructions.

I might be wrong (wouldn't be the first time) but from your description at least part of the problem seems to be MIDI related.

I have a general question.  If if were spurious pitch-bend data wouldn't one see that in an automation track?  I know all of my intentional pitch bend data shows up there.
 
If the pitch bend data is not there then it isn't a pitch bend program right?  If it is there delete it, play the song a few time and see if the problem come back.  If it does doesn't  record another track and see what happens.  If it shows up again it probably is the keyboard.
 
I don't mess with key transposition via a soft synth so I don't know if this actually would apply but if one can assign a MIDI control to it maybe that is the problem.

First of all, I love you guys.  You're all awesome.  Secondly, here's a little update:  I called Cakewalk today, spoke to another tech guy.  Awesome dude, I don't know his name.  He was kind of stumped, himself, considering the sampling rates matched.  He was VERY skeptical that it was Sonar, as were all of you guys.  He asked if I had changed USB ports for my interface - I had done that because I had transported the interface to work with me (guitar instructor) and plugged it into a different computer. 
 
After I spoke to him (I was driving, so I wasn't near my computer), I called my wife to check something.  Just by accident, she unplugged my interface's USB, then put it back into a DIFFERENT USB port.  I get home, laptop is already on from when she had it on earlier.  Keyboard is in tune!  YAY!  Not time for celebration.  I power off.... PRAY.... LOL... computer comes on.... fire up controller..... fire up Rapture.... PRAY LOL ..... choose "grand concert piano" ..... PRAY MORE LOL..... I hit a low E...... SOUNDS RIGHT!  Get out my phone.  DREAM THEATER.  PULL ME UNDER.  Perfect way to check it.  FIRST NOTE.  BOOM.  DEAD NUTS. 
 
Now, time to see what happens in projects.  Big test.  If you guys don't mind checking this thread for another day or two?  I'm going to give the final verdict hopefully by tomorrow.  Please forgive me for not replying to everyone specifically - I DID read ALL the posts and I truly appreciate all the suggestions.  It might be fixed.  If it isn't, I will start going through all the things people have suggested.  Thanks .... thus far.  PRAYING LOL....

Awesome news so far.  Projects ARE working!  At least recording, haven't tried saving yet and reopening yet.  Update in the morning.  Anyone else ever hear of this happening?  Just because of a different USB port?

Another update..... recorded a quick project with my guitar (GR5) and Rapture using my MIDI controller.  Everything was perfect.  Saved it, reopened.  Perfect.  Rebooted.  Opened this project, about two half steps too HIGH.  Yes, it was higher.  WTF
 
Pissed.  Unplugged interface, uninstalled interface driver.  Reinstalled interface driver.  Boom.  Perfect.  Restarted.  BOOM.  Perfect.  Hoping it stays that way. 
 
Conclusion:  it's definitely not the MIDI controller.  It's 100% the interface.  I don't know why it's freaking out, but that's what it was.  Probably going to pick up another one at some point because I can't take the uncertainty of "maybe it'll work today, maybe it'll make my life a living hell for like four days until I figure WTF is wrong."  (I do a lot of recording LOL)
 
EDIT:
 
By the way, on a sidenote, although related to this.... NOT happy with M-Audio.  Bought this in late 2012 in good faith because of reliability and performance of Keystation 88 controller.  A year or so later, M-Audio sells a bunch of products to Avid.  Bye bye support for C-600.  M-Audio sold it, Avid doesn't care.  Product completely in "limbo" and probably forever.  Too bad, awesome interface, would hate to switch to another one.  Oh well.  Thanks everyone. 
 

Lord Tim
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?
 
 

+1 
I had an old USB M-Audio keyboard that was doing exactly that.  When I unplugged it the weirdness stopped. They were no longer supporting or doing driver updates for this keyboard so I wound up getting a new keyboard and everything has been fine since.

Had two M-Audio interfaces. Best things I ever got rid of. Always thought it was me, but it was seemingly never ending driver problems, and I can't imagine the C600 would ever talk well with Win10. Give it the ol heave ho..

This really sounds like a driver fighting with something else to change the sample rate, honestly. Now that we've ruled out the keyboard sending weird data over, that's really the only thing it's pointing to.
 
So again, one last test: bounce down a mix of what you're working on when it's all in tune. The bounced down mix should sound fine when played back.
 
Then, once it screws up again, bounce down another mix then.
 
If that mix is also playing back fine (as opposed to what you're hearing in real time that's out of tune), something is changing things on the fly and we can start to narrow that down.
 
If the bounced down mix is out of tune, however, then something is definitely very screwy.

There was a time M-Audio made good products and supported them with frequent driver updates.

That time was several years ago.