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I'm having the exact same problem. I just upgraded from 2.0.09 to 2.0.13. Now everytime I go into the control panel in a new session, it tells me that it's the first time that I've entered admin, as if it's a new installation.
I'm also having trouble saving my preferences now. I'm trying to close down the site to debug another issue that I think may be related to the upgrade, but I'm not able to close the site. Saving any preferences takes me to a blank white page where it stalls. Going back to the control panel at that point through the URL shows no modules. They only appear once I open the admin module again and get the "first time" message again.
Is this a bug in 2.0.13???
OH! I suppose I should add that my client chose a windows hosting server. YNOTINTX, are you on Windows or Unix/Linux?
[size=x-small]Be the change you wish to see in the world.
-Ghandi[/size]