simpleman
You are using the drum machine 'D16 Nepheton'?
Is Sonar loosing sync with this external device. I will presume so, if that's the case.
I gather you Googled it and got fooled by that mock image of a hardware device.

D16 Group is a software company, and the Nepheton is strictly a plug-in.
Getting back to the issue, my considered opinion is... I dunno.

I can't say I've ever heard SONAR users complain of MIDI tracks sent to the same synth going out of sync with each other. Previous reports of looping issues have always been about soft synths going out of sync with audio tracks and the audio metronome or possibly with another soft synth.
Again, I would ask whether you can reproduce the issue with another drum synth. If not, I'd suggest you hit up the D-16 forum.