I am worried my '06 Mini MCS cabrio rear quarter windows are installed or adjusted incorrectly. They close at different rates and often don't fully open or close as expected.

The drivers side, in particular, seems to have considerable resistance when closing with the top up/closed. In particular, with the top up, the window doesn't go all the way down. It gets stuck about half way. Once the top is fully opened the window can be commanded closed easily. The window seems to be aligned a bit too far inboard. I've tried loosening the forward and aft bolt holding the regulator but it didn't make much difference.

This came up because I've only owned the car a few weeks. Today, the passenger side rear window broke. I took the regulator out and found the wire had popped off the rails. It had obviously been serviced before, too, by a previous owner. I suspect the driver's side is the same way. The car has just over 100k miles. I was able to repair the regulator and reassemble. It seems like a matter of time, the motor groans as it tries to raise the window into the closed convertible top.

 

Had similiar issue on 2005 R52. The person I bought car from told me that rear broken window had recently been replaced by "BMW shop" they take all their cars to. Long story but after fixing tons of stuff this specialized shop had "fixed" on car ... i tackled the passenger rear window that didnt seem to open close correctly based on watching driver side. When up there was also small gap between front door window and rear window.
if you take off trim chrome along bottom of window youll see a round piece with gear looking teeth around it down inside car body. This holds the wimdow in place if yours was replaced incorrectly like mine... ordered special wrench/tool online that made job a snap... i loosened ****? That holds window in place adjusted until in line with specs in my Bentley manual checked gab at front window when up... and boom suddenly no binding when raising and lowering and works perfect ever since.