I'd the same felling of you, but I don't know if I've to check some specific directory, but /extension, /design, and /settings seems configured like the others are, and all other ezpublish options, except this, seem working as intended.
I noticed that installing a vanilla ezpublish, without installing the ezwebin extension, I'm in the same situation.
There is not the option to select the extension for the override, so i think this is what i have to look for.
Does someone know what file "and how" I have to modify them to manually insert the ezwebin extension? (it's already installed anyway, but want to check files) May also this be related to database?
I was right! And I solved this with the help of Salgua.
If you don't see the extensions option in the override page it may be due to the following reason, anyway i think a bug generated that, because I never handled those files, but it seems they was corrupted, this probably happened in the migration of the site 3.10-4.0. Salgua executed a test on the system files, asking if they was modified, the system answered positively, and listed the following files (in my case):
What i did was downloading ez 4.0, and replacing manually one by one the files, a real cache cleaning (/var/cache and /var/ezwebin_site/cache tabula rasa) and than it worked again! Actually salgua is having lunch, than I'll tell you how to have the system check, to check what file you may have corrupted luke.