Found this question today using Google (see below). I have the exact same problem. No replies since that question was posted though.
Asked on September 02, 2010
Lexus GX 470
2006 Lexus GX 470 windows
2006 Lexus GX 470 V8 All Wheel Drive Automatic 145092 miles
After replacing alternator we cannot lower passenger Windows from drivers door
Asked by vicky steiner
Tuesday, December 28th, 2010 AT 6:57 PM