You are correct... it's definitely something to do with the project itself - and is not something within Logic's global preferences.
It could be a corrupt project. It's not common but it can happen.
In Logic 9 you can import all types of tracks, effects, settings etc from one project to another really easily...
In Logic 8 it's more of a 'drag'.
I'd suggest for now, creating a new project and duplicating the number and type of tracks. Keep both projects open and the same time and copy and paste between the projects...
Alternatively, if you wish, you can send me the project and I'll take a look at it on my system to see if I can troubleshoot it. No pressure to do so... if you wish to do this, you can contact me via the Support area:
Just put my name in the title.
Hope that helps