Unfortunately, Adobe does not give us the choice of which images sizes to export. This means that it's all or nothing (of course, we choose all). We really hope that Adobe fixes this in the future. For now, you may remove the offending folders depending on the options you choose.
If you don't use popups (see Popups), you can remove the 'album1/popup' image directory from the exported slideshow.
If you don't use the Full Screen Reformat option (see Extra options), you can remove the 'album1/fs' image directory from the exported slideshow.