When creating a custom page type, with a code name of mycustom.pagetype, Kentico will create a cooresponding table of mycustom_pagetype. Custom tables follow the same format depending on what version you're using. Newer versions use this format whereas older versions prepended customtable_ to the code name.
Regarding syncing the two environments, I'd suggest exporting and importing the individual custom table(s) and page types. Be sure when importing the custom table(s) you aren't importing the data.
As a last resort, if you're not able to import them and there are ghost records or ghost tables, you might want to try to manually create either a record stating there is a table there in the cms_class table or get the schema from the other environment and run the create sql on the database missing the table. Again, these are last resort items and require some knowledge of Kentico's structure and SQL.