Right out of the dealership. When I put the top down it does not complete it's cycle every time. I get the flashing green light and chimes. The top retracts but does fully engage, the windows do not go up. If I put the top up and retract it again it might complete the cycle....such as fully locking up and the windows going up and the green light going out. At that point I lower the windows. Anyone?

 

A visit to the dealer would be good before you damage something because it's out of sequence...

 

Are the windows suppose to go up when top is fully retracted? Seems weird. I do not know any Mini Vert owners. Have nothing to compare it to.

 

On mine (an 06) if I just use the top down button the little back windows will go down all the way and the front windows go down halfway. after the top is down I then have to roll the windows down the rest of the way. I'll usually roll down the windows first then put the top down. The windows should not come back up after putting the top down unless you roll them back up. Sounds like you need to call the dealer and have it looked at.
By the way that is a sweet looking cabrio. I was looking at the same one at my dealer here in CT.

 

Yes, it's supposed to work that way. After the top is fully retracted, all of the windows will go up if you continue to hold the button down. You have to keep pressing the button for that to happen.

However your other symptoms don't seem right and you need to get it looked at.

 

mine wokr this way too..

 

learn something new everyday