Sounds like a ground or power issue, but I don't know where the ground point is. I say this because they require a lot more current to go up than down. If you ground is poor, then the poor connection can't sustain enough current to smoothly operate the motor. Warning that a bad connection can get really hot and that's not something you want to have happen inside a wire harness, or other place with fabric / wire sheath.
I'm surprised that the sunroof AND windows have a common ground actually, but they do have a common power line, so maybe a poor connection there somewhere. Pull any associated fuses, make sure they're clean. After that, I dunno. :/