Convertible top issues...

I have a 1998 E36 convertible. Last time I put the top up the closing sequence was almost complete when this god-awful noise came out of the rear LH corner under the clamshell.
The noise sounded like a dog-clutch jumping or a gear jumping in and out of mesh.
I let the switch go but the noise continued and lite kept flashing.
The only way to stop the noise was to turn off the ignition.
Turned on ignition again and there was no noise but lite started flashing again.
Also noticed that the windows didn't raise again either during the top closing operation. But can raise and lower them ok using the window switches.
Now the lite flashes as soon as the ignition is turned on and if I operate the switch the noise starts again, requiring the ignition to be switched off then on again to stop it.
I'm hoping that it's something as simple as a limit switch not tripping ....
I have noticed that the front windows on some occasions seem to have a mind of their own and start lowering again during the raising operation. Could the two problems be connected or related???
Any ideas please on what the cause is and how to fix this

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This post was auto-generated based upon a question asked on our tech article page here: Pelican Technical Article: BMW Convertible Top Adjustment and Repair

[Wayne 962]

Again, I'm not a huge fan of convertible problems. The noise you heard is bad news, and probably means that something jammed or something became broken. You might try releasing the mechanism using the emergency release under the rear seat and then realigning the mechanism using the technique I posted recently in our forums: http://forums.pelicanparts.com/101-projects-discussion-forum-bmw-3-series-e30-e36-1982-2000/596553-e36-convertible-top-reset-after-manual-pull.html

- Wayne