timmytim,
Do you mean that the strobe light itself misses a beat or two or are you saying that the timing is jumping around?
If you are powering the strobe light from the bikes battery, then after a start the battery will be low and that could affect the operation of the timing light until the battery regains its charge. Also, the engine idle may be inconsistent right after starting and the timing will jump around until the engine warms up and idles smoothly.
The dual oiuput coil produces a positive voltage on one plug wire and a negative voltage on the other. The strobe light works best on the negative voltage wire, but there is no easy way to determine which that is, so just try swapping the timing light to the other spark plug wire.
I recently tried to buy a decent timing light and went through three of them before finding a half decent one which is still not as good and stable as my 35 year old faithful timing light because like so many things these days, they just don't make timing lights as good as they did back in the day, probably because nobody uses one any more on a Saturday morning to check their timing. It's mostly hobbyists and motorcyclist's like us that still use a timing light and we do not form a large exogenous demographic to sway the teenage MBA's who focus only on the bottom line when setting the budget for the teenage buyers.