You could be pushing the open button on the remote when truck is off the open signal will roll down windows if pushed for a while after turned off, I would make sure the remote open button is not getting pushed or also could be shorted to open windows, Thanks let me know if you have more questions, ROY!
This model is not equipted with auto roll down windows. The remote only has door lock/unlock and panic.
If you hold down the open button the windows should roll down try it , let me know Thanks ROY!
I think you have found your problem Thanks again ROY!