From what I can read in your question and the comments, the problem seems to come from the database, not from the theme or a plugin. WordPress users, roles and capabilities are actually saved in the DataBase.
Whenever you install a plugin, that doesn’t reset the things it altered (or you altered while using it), your installation will be left with those changes. Sadly there’re lots of plugins not cleaning up after themselves. Sometimes there’re even themes doing stuff that should (but can not) be reserved to plugins.
A logical (not programmatic) way to debug your problem and find a solution would be to install any plugin that shows you a list of roles and the assigned capabilities. At the current moment there’re already some in the wp dot org plugin repository (role managers and such) or you could write your own. When you got something written or downloaded and installed, your best bet would be to locally set up a plain vanilla install that only has this plugin active. Then manually compare your roles and capabilities and see where it fails or in other words, try to fix the missing roles and/or user and/or role capabilities.
Keep in mind that the existing role manager plugins won’t care about “mapped” capabilities, special post type capability stuff and so on. So there still could be some glitches if you don’t inspect every aspect. Which leaves me with the last note: Go through your backups and install one of the copies where this problem doesn’t occur.