If it is similar to my GR-30, the synth will accept and replicate out-of-tune scenarios (including bends/vibrato which is highly desired). I have not used that in a long time, so not sure of exact settings, but a guitar must be tuned prior to using it.

If the MIDI was not captured (I personally hate editing MIDI anyway), the outputted audio can be adjusted most easily with Audacity. Melodyne most likely would not work well for this edit, but would provide how many cents off the notes are (string by string disparities will get ugly but should have been caught in recording). Once the detune in cents is known, that can be offset using Audacity and keep duration consistent. Melodyne would be worth a shot, but any effects will throw it off. Audacity (or similar) is not a quick method either, so do not assume this is a 5 minute process to fix.

Edit: The "triggering from my keyboard" is throwing me for a loop though. Insight into your hardware setup would help clarify things.

My TriplePlay seems to do very well ... so far.

guitarblah
Working in sonar x3
 
I own an expensive guitar-to-midi synth and I have been using the unit
 
Thanks.

What is the exact model number of your guitar-to-midi synth?  The reason I ask is because the MIDI implementation chart for that device may show you if it is possible to send MIDI commands to perform a master tuning function. 

I use a Yamaha SW1000XG (which is a Yamaha MU100 on a PCI card) which allows the use of specific System Exclusive commands to perform a master tune on all tracks.  These System Exclusive commands adhere to the Yamaha XG standard and work with all Yamaha XG synths and Yamaha XG synth modules. Maybe your guitar-to-midi synth offers a similar way to perform this.  The user guide should show you what to send if it's possible.

Others have mentioned pitch wheel.  I always put a pitch wheel=0 at the start of a sequence and have Sonar set to reset pitch and controllers when it stops and search back when it starts.

Wow I didn't expect to wake and see so many replies.
 
Pitch wheel sounds like the most promising option by far.
I will test that out first.
Also it is a guitar-to-midi synth (GR-20) but as said I'm triggering
it from my keyboard. It does seem entirely possible the keyboard
has settings configured which is altering the cents.
 
A lot of things in this thread to try and it does seem that at least
one will work.
Thanks for the help!

Does the guitar midi synth thing have a global tuning setting, i.e. that which is usually "A=440Hz"?  Is this perhaps not set to 440?

page 13 of the manual for the GR-20 "You can adjust the reference pitch in a range of 427 Hz–452 Hz. When the GR-20 is shipped from the factory, this is set to 440 Hz."

rabeach
page 13 of the manual for the GR-20 "You can adjust the reference pitch in a range of 427 Hz–452 Hz. When the GR-20 is shipped from the factory, this is set to 440 Hz."

That relates to the unit's guitar tuning function not the pitch of the midi banks.

So, as far as I know, there is no MIDI function or controller to fine tune pitch.
 
There could be a SysEx message going to your synth that is altering tuning.  I have had SysEx messages I didn't know about in another track for another synth that was using the same device number.  If you can't get any other resolution, you might read the Sonar help on SysEx and make sure that is not the issue.  If it is, you can delete the SysEx messages and reset the synth.  (How did I get SysEx messages in the sequence without knowing?  By recording MIDI from a synth and pressing a preset button that sent SysEx to Sonar.)  If you check the tuning of the synth with a tuner, then--with Sonar close--reset your synth and check tuning again, that may shed some light on whether the synth itself has been set to a different tuning standard, or whether there is something in the track that is sending tuning information.
 
Finally, there is a discussion about sending fine tuning messages to a synth at this link:
http://forum.cakewalk.com/how-to-detune-MIDI-m1858470.aspx
 
Just to clarify, MIDI itself just sends notes, not tuning; but MIDI can be used to send system exclusive messages to a synth.   Confusing, right?

The pickup used for my GR-30 has a 13 pin MIDI cable, so the unit does accept and process system specific messaging. I honestly never tried a keyboard to drive it, but Konrad's comment to zero pitch bend is worth trying. I have seen that wheel drift on older controllers. Barring that, it would seem the pitch delta is being done inside the GR-20.

Can also shoot Roland an email asking them specifically.