im no guru (or SQ guy at all) but goingdef's suggestion makes total sense.
if you are getting windshield flex from your sub that means they are pushing all the pressure to the front of the cabin, conversely the mids/tweets are doing the exact same thing at the exact same time but are pushing towards the sub (in a sense).
If you have enough pressure in the cabin to flex the windshield then you have enough pressure to keep the cones on the mids/tweets from moving properly. by switching phase on your subs they will be pressurizing the cabin at the exact OPPOSITE time as the mids/tweets, therefore allowing the mids/tweets to time to move to create the vibrations needed to produce sound.
i would think an easy test for this (if you dont want to mess with the sub wiring right away) would be A. turn of the sub completely or B. open all the doors to equalize cabin pressure. If during either (or both) of these tests your mids/tweets sound like they should then goingdef's suggestion is the proper fix.