Have you TEMPORARILY bypassed the window relay to see if that is the problem?
(Bypass it only to 'check it out' and see if that is the issue, if it is,
you need a new relay)
You know power windows have a relay that will 'pop' up a little red
button on its side or top if the power window button is held down
or up to long? This is to prevent the window motor burning out, etc.
The relay should be located under the hood next to the battery box
or in the fuse panel located within the dash of the passenger side
(Well that is where they are on my 06 Premacy anyhow).
If it was the window actuator motor, Id think itd go out and NOT
come back on, what you are describing to me sounds like that little
relay gets hot and the plastic on it expands essentially separating
the circuit. No?
Good luck either way!
Peace!(rei)