Has anyone figured this out yet? From what I understand, the backpack is not a physical storage, so when BrokenItemsCleaner runs, it cleans up the backpacks as well which breaks the guns.

My recollection is that this was resolved a long time ago when I updated the backpack storage container to use a physical entity (under the map), but the issue was reintroduced for pages besides the first page (when backpack pages were added) since additional pages used the same physical entity and were not discoverable by Broken Items Cleaner, but again should have been resolved in v3.13.0 since we made every page have a physical entity.

It's not really my intention to support Broken Items Cleaner, though, as it has other shortcomings. It really needs to be replaced with a different implementation.

I'm not sure how necessary a plugin such as Broken Items Cleaner is today, given that a recent Rust update ("Bags To Riches") optimized the item entity logic to only create them when in a player inventory (see the note about planners).

Reduce server side entity counts by selectively spawning Planner entities

I think I figured out a way around this by only running brokenitemscleaner at startup and having timedexecute unload it right after, because i haven't had any complaints since I started doing that. Which means it only affects players that are online with guns in their backpack?

The part that's confusing me is that it shouldn't even affect this plugin. It probably affects the vanilla Backpacks though, as Broken Items Cleaner does not search inside items last I checked.