Huh. So… I created a new project, based on the one I was having slow-save-time issues with. I saved it as a template, then deleted all the audio from the pool, brought in new audio (different show but same mix layout), dropped it in the project, added video, did lots of edits etc.
Saves in this new project are near-instantaneous and have stayed that way no matter how much more complicated it got. Saves take one or two seconds max, rather than taking nearly a minute to save as the old project did. It has almost as many tracks, just as many plugins and groups and effects.
So, what can I say. Weird.
Over the next few weeks I’ll try to investigate when the opportunity arises.
The only difference I can think of right now is that the new project was built from scratch in N6.5 (albeit based on a template created from the problem project) whereas the old project started out as a Cubase 6 file opened and edited in N6.5.