Custom post type ‘Show on screen’ didn’t apply to number

I used your code and I wasn’t able to re-create the error – it seems to be working correctly for me on a fresh 3.5.1 install.

Does this also apply to your other screen options, specifically the checkboxes for columns to display (comments or dates) ?

If applicable, try deactivating your plugins and seeing if that clears up the issue – this is the only thing I can offer for the moment.