That setting is stored in user defaults, not part of the document. It's mostly managed by Apple's outline component... I just give it the name to save under, and then it automatically updates defaults when items are expanded/collapsed and should restore those settings when you next open TaskPaper.
The values are stored under "NSOutlineView Items Sidebar". This is what you should see:
When you expand/collapse items in the sidebar you should see the defaults file updated a few seconds later. (Maybe switch out of TaskPaper to force it to update the defaults file if it isn't.
If it's not working I guess a few things to check/try:
- Are other user defaults settings not working?
- If not maybe try quitting TaskPaper and deleting your existing user defaults file so that it's recreated.
- If still not working what happens when you try from guest user account?