While testing various things around #565, I created a new custom entry (for /Users/Shared/) and it won’t go away. When I remove it, it disappears, but it’s always back when I relaunch.
I tried removing it with B61 and got the same behavior, so this isn’t related to the post-B62 changes.
It could have been induced by me having to manually restore Catalog.plist several times, but I don’t see how. I can dig into it when I have time, but like I say, I’ll be concentrating on plug-ins for a while.
I just reproduced this, but then got it to work.
It seems to me like it's the same kind of problem with saving triggers.
If you change to another prefs (e.g. triggers), close prefs, open prefs, click catalog this will write the catalog to the .plist and it should then be saved for next launch.