If you say you've done this same process (standalone -> export -> SONAR ->import) and it always works then it simply has to be that this song has something about that has corrupted the exported MIDI.
I know I know, I'm being Captain Obvious here.
That's about all I can think of as I never use the standalone to create parts. I use the VST in SONAR and copy the song arranger MIDI into SONAR from the VST and then delete the MIDI in the song arranger.
Once and only once did I ever (for shins a grittles) did I copy the MIDI from SONAR back into the VST and I will say it sounded "different" bu not anything like you are describing.