I have a problem with 1Password 3.5.9 which is that the folders keep disappearing on the left, leaving only "All" and "Unfiled" smart folders.
The solution for me is to "Clear Cache" in the Help menu. This shows the folders again and they remain showing while the window is open but after a few opening and closings of the window the folders soon disappear again.
I've tried "Reset Folder Permissions" and "Rebuild Data File" but these don't bring any solution.
It is a puzzler for me.
I've searched this forum with "disappearing folders" and "folders disappearing" but it hasn't brought up any postings discussing this issue.