If you're running shorter cranks you'll need to raise your seat up compared to your other bike. If your knees are bugging you, you might want to consider a lower ratio. It might help to play around with your position on the bike too. Is it both knees or just one? Bearing in mind that they don't like your road bike, it might mean that your road bike isnt' fitted so well to you either.

I would have thought it was easier to keep a constant speed on a SS, seems it is on a fix.