I get them with certain shorts and don't with others. I don't get them in my Performance brand bibs, but I do in my MTB shorts with I'm riding the fixed with them. Then again, I don't get them with those same MTB shorts when I'm wearing them on my MTB.
I believe it's a matter of not being able to get out of the seat as much with the fixed gear and coasting. On my MTB I spend half the time sitting and half the time out of the seat, so maybe that's why I'm not so affected by it on my freewheel bike.
Do you use a chamois cream? That helps me a lot.