Thanks for letting me know. I'm not really sure why the game seems to be issues caching the persistent data. Unfortunately that's baked into the renpy game engine itself (especially since it also affects seen dialogue - that is definitely part of the engine functionality) and isn't my code specifically, so I'm not sure it's something I would be able to fix even if I could recreate it.
With my last game I've had scattered reports of things like this happening - as well as some other funky issues that seem to be renpy specific. Those are always frustrating since there's not much I can really do about them.
I'll keep an eye out for it just in case, though! I'm glad to hear you found a fix for the problem!