Mwah
I’ve had similar problem with the 2016.08. In several projects, I’ve been hiding a folder of unused midi tracks with the ”in sync” option selected at the Track Manager window. Whenever I re-open the project, the hidden tracks are un-hidden in the console view but stay hidden on the track view.
The more I look into this, it seems to be something to do with the "Global options - Keep track/console visibility states in sync" button. I have always had it turned off. It's a global option, so it doesn't get saved with each project, correct ? Somehow, it is getting turned on . . . is there a key command that I may have hit by mistake to turn it on ?