It's all about keeping the knees warm. I've started to use leg warmers as my new commute presents me with a big hill early on.
I also consciously take it easy until I feel my knees warm up. I keep the cadence high and relaxed. That first 0.1 of a mile - it's important to be careful.
You should also be careful if you miss a couple of days of commuting (even Mondays can be bad if you spend the weekend on the couch) - the knees seem to be sensitive to getting out of shape.