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Bummer. I think there might be a relay if you haven't already looked at that. It could also maybe be your ignition switch, it can cause all sorts of weird issues, though I'm not sure if windows are part of that equation.
Have you tried disconnecting the battery for a few minutes to see if they reset? Does your alarm/central locking work? If it does, does it beep or anything on actuation? It shouldn't. All you should see is your lights blinking and central locking do it's thing. If it beeps, there is a problem. In the owners manual there is a section that explains the beeps and what they mean. I just don't remember or have the manual handy.
Also, you mentioned this happened after raising and lowering the top. Have you tried it again? It could be the center latch isn't completely closed, or the top isn't quite properly seated. Open and close the top with the doors open, then see if your windows move down then up upon lock.
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