Brandon,
I assume by the custom table you mean the content table that contains extra fields for your custom page type.
If it's there in one instance, but not in the other, the only thing i can think of is someone or somehow the table was deleted. You may need to recreate the table manually (you can go to your production database, right click on the table and generate the create script table), then once that table exists, try a full sync from your production environment of those pages, hopefully that will re-populate them.
If you are looking to delete that page type completely, and for some reason only the database table deleted and not actual page type, you can look to manually delete it from the CMS_Class table, although manual processes like this wont' be caught by staging.