Have they checked the PCM connector and wiring harness. This may be caused by water getting into the PCM/harness/connectors. There was a post on a recall for water getting into the pcm and corroding the harness connectors. PCM seals mis-positioned and leaking. Since the pcm talks to the other module it may also affect the windows? Not sure if the recall affects your particular vehicle but it may be worth a try.
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