I just updated to 3.9.1 and it does seem to solve the problem of adding items to folders and deleting folders.
But the other issue I mentioned previously with the 1Password menu bar still seems to exist. I just created some new test folders and these still do not appear in the "Go & Fill" drop down list from the 1Password helper icon in the menu bar. And a reboot doesn't seem to help.
Also I'm a bit disappointed to find that this update seems to have broken the option to download previews for login items, but it seems like this has already been brought up in another thread