Apologies for taking so long to get back to you. The internet on my island has been down the last couple of days so this is the only chance i had.
Anyway, I made a fork of the plugin https://github.com/BinaryGeometry/custom-post-type-ui/commit/94c86b91c9702ff9203fa0e3703ce10359120214
So you can either download the new custom-post-type-ui.php file, or else look at the commit message to see what changes you need to make to the plugin you have installed already.
Basically all we are doing is adding a single key pair onto the end of the arguments array for the native WordPress create_custom_post_types() function.
I can't actually test it as I don't have WordPress installed, but let me know how you get on if you would as I would like to push the changes back into the original repository if you find that this solves the compatibility issue you where having.
- 'labels' => $cpt_labels
+ 'labels' => $cpt_labels,
+ 'show_in_nav_menus' => true