As stated in the subject, all bundles are active in the resource manager. I don't want all of them loaded so I deactivate what I don't want to use. When I re-open Krita, all the bundles are active again.

I remember that Resources management used to have that sort of problem but it seems to have been fixed in version 4.1.5 as I've just tested using the 4.1.5 appimage. What version of krita are you using?

I have tested this both with 4.1.5 and the 4.2 preview appimages. No difference between the two.

In case it's a strange profile/configuration fault or something in that area, have you tried backing up your config files and resource folders and then deleting the originals to try a 'fresh start' to see if that clears the problem? That is drastic but it's easy to do (and easy to restore) and it's the only thing I can think of.

Alas, I tried it to no avail. It's quite stubborn.

OK. I have resolved the issue. The problem is with the Appimage itself. Because it's using it's own tmp location that's under lock and key, it overrid any adjustments I made (IE, resource bundles used, Brush groups and so forth).

I tossed the appimage and went with the PPA installation and now the actual local settings are used.

Ahhh, you tried to deactivate the default resources. The appimage has those in a tmp folder with a random element to its name, which changes on each restart. So the resource is blacklisted by location but the location name changes (and hence the blacklist entry is invalid) on the next restart.

I don't know why it's done that way but that's how it is.

It's one of the reasons I'm rewriting the entire resource management system...