Personally I have a strong feeling it is something in the console end, as i do things like this all the time, and have never had an issue with it doing what it should, when it should. Even when changing lots of parameters at the same time, it always keeps up. The only time I ever see some sort of a puase, etc is when loading a large file for the first time.
I have had issues in the past where doing just what you are trying to do, and when I had problems it had to do with what information was stored in the previos/next cue etc. Or soemthing else running had something stored in it that cause the jump etc.
I would definitely be lookin got the board more than anything else.