I have the same problem since I upgraded from 3.8.6 to 3.9.1. I have also empty drop down boxes under Setup -> Ini Settings > "choose siteaccess". So I can't edit my setting only at the moment.
I've had the same problem and solved it setting the RelatedSiteAccessList, defining each siteaccess that use the same db. Then all of them appeared in the admin.
(Note: if you check kernel/settings/view.php you can see that this list is used to make the menu shown in the admin, at least in 3.9.2)
hth!
--
Xavier Serna
eZ Publish Certified Developer
Departament de Software
Microblau S.L. - http://www.microblau.net
+34 937 466 205
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