Foxmarks won't sync and other bookmarks issues

At first I thought I was having a Foxmarks issue, but now I think I'm having general bookmark problems.

If I bookmark a page and just add it to the general default folder, it shows up in the Bookmarks dropdown, but it does not show up in Bookmarks --> Organize Bookmarks.

When I bookmark a page and choose the folder, it lists folders that aren't actually available anywhere else.

Regarding Foxmarks, I have tried to do a "Force overwrite of local bookmarks" but no bookmarks are added even though there are no errors in my Foxmarks log.

I'm not really sure what's going on and what I can do to fix it, so any help would be appreciated.