I just updated the exporter script today. It now shows you the associated texture number of each texture, as well as some other under-the-hood improvements.
That explains it; thanks! This is a great tool BTW, thanks for all the hard work you've done on it.The exporter handles smooth groups as you'd expect. If you use the exported mesh ingame, the smooth groups should be intact. You can mix smooth and flat faces on the same mesh.
The importer doesn't detect smooth/flat faces right now, unfortunately. You'll have to re-do the smoothing yourself.