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I realize this is an old topic, but I was pointed here by someone else.
I am having very similar problems now. My System Admin icon dropped out early this morning after no major change. I tried reloading the module as you had directed above, and I still don't have the icon. I checked all the cache folders, and they are all set properly with the correct permissions and what-not.
Is there any other solution that perhaps I havn't tried yet?
Incidentally, I'm using XOOPS 2.0.3 on a Debian Linux server with all the current versions of PHP, mySQL and so on.