I've tested it just now and it is working for me with and without Mom's Box.
It might have an incompatibility with some other mod you are using?
Are you able to send me your modlist (either via a collection/a screenshot of your mods folder/something else) so that I can test all your mods and see if it happens for me?
If it is an incompatibility with another mod I might be able to fix it.

something is definitely wrong then, now that i knew what to look for it didnt seem like the sand was going down after clearing rooms at all (i got it again without mom's box on a different run, it did eventually drop stuff on the first run)

definitely a bug of some kind. it must have only been going down after waves instead of after clearing rooms or something.

It shouldn't take twice as long, it should still be the same amount of rooms, when you clear a room the trinket sprite should update (the "sand" from the top falls down to the bottom, 2 pixels per room), after 22 rooms all the "sand" pixels should be at the bottom of the trinket and your items should spawn.

Does it take twice as long to drop stuff when you have mom's box of stuff? Because I feel like I must have cleared at least 30 rooms by now (including all of boss rush and two whole floors) but nothing has dropped.

Very interesting concept, well done

It does not

And if you drop it? Does it start again from the beginning?

Ah yes, I just looked that up.
I didn't know the souls had different personallities.
I chose red because the item gives you curse room items, and curse rooms usually require the player to get hurt, so I though red "blood" would be fitting.
I am planning to do a small update the mod when I get free time (make it so you get two charges in L shaped rooms and the O shaped rooms, therefore the trinket will be consistant to when you get battery charge).
I could provide alternate sprites in the folder, but the folder would need to be renamed manually.
It may also be possible to make a mod that overrides the current mod's sprites, it would be a seperate mod that could be downloaded.
If anyone wants those then I could easily do either.
Or if you don't want to bother me you should be able to edit the sprites manually (although I'm not sure if steam would keep the changes or override them when you launch the game)

and then the undertale fans came a demanded you make it the light blue human soul

Thank you, I can't take credit to the idea though, it was my friend's idea - I decided to learn how to mod so that I could create his item.

This is a cool idea! risk reward and all that