I think that either your mod has some extraneous changes unrelated to pausing or you may be missing some bug fixes in your mod and should recreate it based on the latest version of the official file. (It'd be good if it was made in a way that didn't require overwriting any game files, to avoid overwriting official fixes, etc.)
Good lil mod, and it works. But I'm wondering: time passed when you entered and left towns, and I figured that was an intended feature. This mod seems to remove it. Could I get some insight from ya, if you have any?
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