Problem: Noticeable pitch changes when creating and importing/exporting stems.

It sounds very much like a clocking mismatch somewhere. A file recorded at 44.1 on a system referencing a 48k master will be the wrong pitch when played back on a system referencing 44.1. Double check your wordclock settings: if your master clock is running at 48k, but your Sonar projects are at 44.1, that would be the source of your problem.
 
Have you tried importing the stems back into the original projects to compare? And, are all your collaborators noticing the same problem?

McMoore11
Anyone else notice this?

 
No is the simple answer
 

Lately when I create stems to send to collaborators or session players,  my files that they receive are a quarter step flat.  I have the Manchester update and have all my sessions running at 44.1 24 bit.
I can't think of a solution to this other than trying to pitch the stems a quarter step sharp prior to exporting them and hoping for the best.
Anybody got any ideas?

 
Make sure your collaborators are also running at 44.1KHz because this sounds like a classic sample rate mismatch
 

Razorwit
Yeah, sounds like a clocking thing. I doubt it's 48 to 44.1 because that results in a change of about 1 and a quarter, but it could be a smaller sampling rate discrepancy. I'd drop the word clock and see if it continues. I've gotten some funky word clock stuff from time to time.
 
Dean

Yep. I used to have an Echo Audio Layla 24 that turned out to have a clock that was just a wee bit off-spec. When I hooked up my old Tascam DM32 via ADAT, I caught the problem: the DM32 has a utility that tells you how much the incoming clock is deviating from the target rate, so when I tried to use the Layla as the master, the DM32 let me know the sample rate was 97% of 44.1k.

So off to the expensive world of proper master clocks I went (and dumped the Layla in favor of RME )

Back to your OP, Mark - the quickie test is importing the stems back into their respective projects. If they line up on your system, that implies a clocking mismatch between you and the other folks. The next step is taking your Black Lion out of line like Dean suggests. Export stems using the MOTU as the master clock, and send 'em to someone offsite to check. And like Jonesey said, also double check *they* are using a reliable clock set to 44.1....
 
Black Lion has a good rep, but my first guess would be the problem involves the Micro Clock. The Micro Clock MkIII seems to be a genuine competitor to the higher-end master clocks, but I don't think the earlier versions are quite in the same league. Regardless, whichever device is causing the sample rate deviation, something ain't right somewhere for sure.
 
Good luck!

Youse guys are awesome.  
Conrad, Dean, Jonesy, Hambrecht, Chuck,
Thank you.
And Chuck it wasn't the pitch knob so much as the suck knob.

Hey Brundlefly,
All instruments were tuned 440.  The problem arose when I set up my session at 48/32 and then transferred the 2 track of the bed or rhythm session to a new overdub session to record the vocals set at 44.1/24.  I work in a new project or session to avoid latency issues for the vocalists.
I then took the vocal comp and imported it back into the 48/32 session for mixdown and the vocals were +51 in pitch.
I retuned the vocals down -51 in stand alone Melodyne.  Problem skirted.
I also found that 2 of the session players I work with have their ProTools or CuBase sessions set at 48.  I need in future to make sure I include the sample rates info along with the track information.
It's always something.