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MySQL root Grants Broken Following a phpmyadmin Install in Windows

So this is a weird one. I recently installed phpmyadmin 3.5.1 in a MySQL 5.1 / IIS 7.5 environment. Everything was going well until I realized that following the installation (which was fully functional) I could not login to MySQL (from the CLI) without referencing the hostname (-h flag). I figured that maybe the .sql script included with the installer messed with my grants, but a quick show grants revealed I still had the same permissions granted to root as when I started. So I figured that I would update the grants on root to what was displayed in show grants just in case. This produced an insufficient permissions error even though root had "full" privileges. To resolve this I added skip-grant-tables to my.ini, restarted the mysql service, logged in as root, flushed privileges, and again updated grants to what was displayed in "show grants". I then removed skip-grant-tables and restarted, and I was again able to login locally. I'm still not certain what caus