I use MySql5x under Linux but also have a MySql5x windows version that works fine too.
Sometimes the smallest/dumbest things will throw you, and the error you see is not really the error at hand.
In my Linux, EqEmu wasn't seeing my Perl as it should, and also , I had some Libs missing.
For windows, EqEmu likes mySql to be installed in c:\mysql\ (MySql4x installs to c:\mysql\)
MySql5 install defaults to c:\program files\mysql\, so I just force the install to c:\mysql\ . This might help, mostly if you use the cavedude installer. Probably not a matter, but I'm just telling you how I have mine running.
Also, make sure your Perl is properly installed.
Did you update the *.conf files? the newest ones are always in the source/utils directory , but probably already updated in the windows package.
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