OK Rick, got it.
First, you could also start this same thread over in the "tech help" forum, you may also get some responses there.
What I am leaning towards is this, and I know it won't make a ton of sense, OK?
Sometimes I've seen this happen, and what MB advised me to do it totally disconnect the control module for the soft top and windows. This is one module (does both jobs) and is located behind the passengers seat, inside that storage compartment under the false floor. You need to remove 3 10mm plastic nuts to remove the false floor, then you'll see the rather large metal control unit, it is I believe equipped with 3 electrical connectors, hopefully you know how to remove these connectors, has like a sliding latch on all 3 of them. Usually you need to remove the nuts that hold it to the floor to release all off the connectors (it's a tight fit, you'll see). Don't turn the key on while doing this, keep it off until you're done. Just disconnect all the electrical connectors, plug them all back in, bolt it down, then try it.
Before doing this, can you tell me if the "express down" feature of the windows is working OK? If not, I would give synchronizing the side windows one more shot.
Let me know how it's going.