Hello,
I think I know where is the problem, can you try in your Custom field configuration to remove in the Restriction part the Categories selection ?
And see if that work ? You have to know that this part create restriction to display or not it in the product configuration page.
Filter can't be used on restricted product categories (too way complicated to manage for a filter system...)
Plus if, you don't set product custom field in your product config it won't be display in front end.
If you want restrict the Filter use with this product custom field, the restriction have to be in Filter configuration page.
Hope this will help you to solve this and fit your needs.
Regards