Are you currently using Custom Item Definitions?
From the behavior you’re describing, this appears consistent with how that plugin modifies item data. It dynamically creates custom item instances, which can cause stacking logic to behave differently or produce unexpected results.
If you are running Custom Item Definitions, that is very likely the source of the issue.
For clarity: I do not officially support integrations with Custom Item Definitions or other plugins that fundamentally alter item definitions. Because those plugins modify core item behavior, they can conflict with stack logic in ways that are outside the intended scope of this plugin.
If an issue is confirmed to originate from Custom Item Definitions (or similar plugins), I won’t be implementing compatibility patches specifically for it.
If you'd like, you can temporarily disable it and test again that will confirm whether it’s the root cause.