I agree this sounds counter-intuitive, but I've run into the problem before. Last year my Jawa started acting up in this manner shortly after I had played around with the clutch (the starting clutch had gotten grease onto it, and I had to clean it out).
I presumed, since the starting clutch was working, that I had fixed the problem. When I started to experience the symptoms that Dave described I assumed it had to be something else. After about two weeks of cleaning carbs, decarbonizing the engine, checking wiring, etc. I decided to clean the drive clutch. Problem disappeared.
I don't think the clutch was slipping completely, I think it started to slip when it reached a certain load. The engine would lose power sooner when I was going up a hill, and not lose power at all when I was going down a hill --the load seemed to affect the problem.
I can not be 100% certain that the problem was the clutch, but cleaning it out did fix my problem and it's the best theory I've got.