So I got the time dependence to work, but I'm not sure what went wrong in the first time anyways. I'll trying to get a sense of how long it takes for the temerature to semi-equlibrate, and coming to grips with comsol as a whole. There seems to be some inaccuracies when the timing increases, so I'm having to figure out how to increase accuracy without drastically increasing compute time. On the bright side, I switched the model to heating via deposited beam, for a more accurate model.

Attached is comsol's handling of a deposited beam modulated sinusoidally with a frequency of 0.1 Hz and screwing up badly.  Y axis is the average surface tempurature across the whole disc.