We own a '93 300CE Cabriolet and have never had any problems with the top/window system working as it should.
Could it be that your convenience control module (windows)it starting to go? If you have the service manual CD (disk 1) you might want to check out the relay_control. pdf., within that file, check page 2.5, figure 20, part id N57. Maybe it could be a starting place. Since it sounds like your top works fine I don't think there would be anything wrong with the power top module which you can also find within the file I mentioned.
Have you checked the electrical connection to the switch?
If you don't have the CD let me know and I'll e-mail the pages to you.
Hope you can get this figured out because it really is a great car. My only wish is that they had put the power of our 400E under the hood.