I have a CPT "credit". The "Screen Options > Pagination" show the value of 20. When I change the value to something different and save, it reverts back to 20. I"m able to change the Pagination of the Media Library or Pages. I've tested this on a staging site with a different theme and all other plugins disabled, except Meta Box and Meta Box AIO.
Hi, I can't get it to work on the current site. But I spun a new test site and was able to get the Screen Options updated on a MB CPT.
There was possibly an issue with one of the taxonomies associated with the CPT. I was using a taxonomy slug "type" and it wouldn't work when exporting to another site. So I spun up a brand new site and tested that tax slug with CPTUI plugin. It gave me an error: "Please choose a different taxonomy name. type is already registered." Default 2021 Theme and no other plugins.
I tested with MetaBox and it didn't show any issues with that Taxonomy slug.