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Strange, just when here to post about the same.
Upgraded a module (WF-Section) via FTP sync, and now my SysAdmin icon is gone from the Admin.php page. Alias, I have 'Administration' in the User menu, but the System Admin icon is GONE from the 'Control Panel Home' menu.
Using /modules/system/admin.php works, but what happened to my Menu?
Any scripts to 're-install' Xoops?