Yes, unfortunately it didn't went so well as we expected. Because of the naming mistake WordPress isn't replacing the files in the old plugin directory but creates a new one. We're working on fixing that ASAP so everybody could safely and easily update their Gantry. Right now a solution is to remove the plugin directory and install it from the package at http://gantry-framework.org or just from the theme download directory.
I'm very sorry about that and hope that we'll be able the sort this out really quickly.
Thanks,
Jakub
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