I've posted a new start-multiverse.bat file that resolves a particularly debilitating bug when running the server on windows.
Make a backup copy of start-multiverse.bat in your multiverse/bin folder
Please download start-multiverse.zip
Unzip the contents of the zip file into your multiverse/bin folder
You will need to clear out the plugin_status table in mysql.
To do so start the mysql command prompt.
Login and execute the statement
Where MV_HOME is the directory of you server/bin folder.. e.g. c:\multiverse\bin
Once you've cleared the plugin_status table run start-multiverse.bat