It is far more common for a guitar to be out of tune than a synth. And before you go too much further, it would be a good idea to find out what the other instruments are actually tuned to. My guess is that the engineer and guitarist have decided that you have somehow created a sample rate mismatch, recording your synth at 48 KHz but saving the wave file at 44.1 KHz somehow. That is the only reason I can think of that they would even mention the sample rate.
That sample rate mismatch would also change the speed of the recording not just the pitch. Anyone who calls himself an audio engineer should have been able to change the sample rate on your file to fix that mismatch if that was the problem, with only minimal loss of quality. I actually do not know how to do that in Sonar, but it is easy enough in Audacity (free download)--just import and change the rate under set rate in the dropdown menu that appears when you click the black triangle to the left of the tracks), then tracks>re-sample and then export as a new wave file (WAV (Microsoft) signed 16 bit PCM).
To figure out why you had the problem in the first place it would be helpful to know more about exactly what you were doing to get there. What kind of synth are you using? Is it being controlled by Sonar of is it just that the synth output is being recorded into Sonar?