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This bug can be reproduced with StackUp! installed and configured for stacks over 64 items.

I'm not going to bother with mods that do weird shit like this. I'm afraid you'll have to disable that feature.

I can replace that, maybe it'll fix it.

I'm no longer maintaining my 1.12 mods, sorry

Found the root of problem - you hardcode stack size - https://github.com/Vazkii/Quark/blob/bef6b57daf94c0506514616056a556fc674685ab/src/main/java/vazkii/quark/base/handler/DropoffHandler.java#L272

When actual stack size can be different (and bigger than this value). The issue is definitely on your side.

But as asie stands, any issue with his mod <-> other mod needs his attention @asiekierka

Unfortunately that did not fix the issue, though I understand if you do not want to support StackUp. As a workaround I've installed InventoryTweaks.