Well, seeing the behavior is the same wether you edit using admin or trac.ini directly, it certainly can't be an issue with custom fields admin plugin as all it does is edit trac.ini for you. And, it can't be Trac itself - that I'm also quite sure of.
What then remains is the reason those fields are there in the first place, and what piece of code demands you to upgrade - and then actually puts the fields back in the file. By the names of the fields, I suspect it would be a plugin that works with ticket dependencies or hierarchies. In Plugins webadmin, try to disable the most likely candidates - then try to remove the custom fields again. Of course, if you actually use the 'problematic' plugin, then deleting the fields no longer seems like a good idea...
Anyway, can't see that it is an issue for CustomFieldAdminPlugin itself, so I'm closing the ticket. But please reopen and move to a different 'Component' if your continued quest leads you to bugs or feature requests for some other plugin.
