I'm sure you already saw the bypass I used on the 3d Forum, but I'll put it on here for the benefit of others having the same frustrating problem. Worryingly there has been total silence from Magix support since I asked them about it a few days ago
My left/right clips were filmed and imported as 1920 x 1280 16:9 avchd clips. I added transitions and a title, then exported as a movie from the top toolbar 'File' menu. I used the Mjpeg settings at 1280 x 720, 3d side by side. The finished file would only play in sqashed S/S as we have found, so I opened the free StereMovieMaker programme http://stereo.jpn.org/eng/stvmkr/index.html I imorted the file as a 3d movie at 50% on the drop down box. SMM reads Mjpeg files well, so I set the viewing to the format that I wanted to export in, side by side crosseye. I then exported as a stereo file using an mp4v2 codec from the list.
The resulting file plays fine in Windows Media Player and other programmes.