We never met with this problem before, so I guess certain settings are not correct in your project. Could you send your project to us to check? If it is too big, upload it here http://www.mediafire.com/ and let me know the download url. Thank you.
Jenny Zhao from Easypano
I deleted the second map and scenes associated with that map then saved the tour under a slightly different name. I then re-imported the same map and a few scenes and everything worked fine. Its when I link the second map to a button on the main window that the hotspots disappear. Unfortunately, this tour is protected under PCII and I am not allowed to let it be seen by the public.
Found the solution: In TW3 when linking a button to a map I use to first under "actions" link the button to a map and additionally link the button to the first scene for that map (so two links). With TW6 it appears that I only have to link the button to the first scene for the desired map. Anyway, hope this helps if someone else comes across this issue.