Should not have anything at all to do with jump start.
the windows work, by pressure to move them, in auto, so if anything in way, they stop. However, I would think low voltage would give the same.
SO why did you need to jump start. Battery flat. WHY
Is your alternator working correctly, charging battery. If not, not enough voltage for windows, and eventually not enough to keep car running, will just die.
SD, April 2012