It could definitely be the sub folder, yes definitely. Using a sub folder makes the multi site much trickier.
If its working then roll with it.
Looking at the site, it seems like everything is working, and I mean everything as the pages of the subfolder seem to be working as well. All with the new flash app you have.
[ed. note: nuan88 last edited this post 7 years, 10 months ago.]
Thanks @Goldsky for the overview, it is quite helpful
The subfolder is now gone/empty? It could be htaccess if you haven't changed it