Hi Martin,
Currently Photosynth panoramas are cubes only, and the new ICE has been modified to stitch cubes when you export to Photosynth. There's no support for other panoramas (spheres or cylinders) yet--that would have to come by either Photosynth taking spheres and cylinders, or hdmake re-projecting them to cubes.
If you have the original images you can re-stitch them in the newer, faster ICE and upload them that way.
--Howard