Re-read my post #20 this thread. Generally speaking, yes, any smoking cause by the side stand should stop after a short while of riding.
However, you mentioned that the bike leans a lot when on the side stand and Commando's wet sump if left sitting. So, you might get a lot of oil where it doesn't belong, carbon up the cylinder a lot and be confused. That's why having a look in the cylinder might shed a light on what's wrong, but I don't think that's the problem.
The problem is that when presented with the impossible/unlikely in a forum thread, each person must rely on their experience to try to help. You have an impossible/unlikely problem. There are only a few things to eliminate. No point in me saying mine again or reiterating what others have said.
Feel free to look at my signature, go to my site, look at the bottom and call me. Sometimes it's easier to work through things on the phone instead of in a thread.