Not sure how reproducible this is, but thought I'd better post immediately before I forgot about it -
I just logged in one of my "Project Characters". When her status on the site changed to Online, the Project flag disappeared!
... Oh, this is interesting. While still logged in to the game, I edited her profile and saved it with the flag back on, and then a second profile appeared on the site. Interesting ...
(I then deleted both profiles and let the system make a new one, then edited it to flag it a Project profile. Still logged in, seems to be OK. The character is Cosma Nova if that will help you do any research.)
Hmm, interesting. I'll try and get this to duplicate today and see if I can't trace down what's going on.
Glad to see people are using the new TNT at least! :D