9x out 10 it's going to be the something with the regulator. I replaced a 4Runner driver side a couple of years ago and just did one on another car last week. Could be as easy as a loose nut and it's jumping around. Or not. Good news is the regulator can be had for under 50 bucks on Amazon. The bad news is the motor is going to run you over $100.
http://www.amazon.com/VDO-WR51038-To...1&s=automotive
Just never know until you get the panel off and get a look.
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Yeah, what he said.
Let us know what you find out.
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