When you select "Startup Variables" in the free "MySQL Administrator" you receive the error: "Access violation..."
Quickly looking into this, it looks like MySQL Administrator can not find the my.ini configuration file.

Solution:
Editing the "MySQL service" registry settings at:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\MySQL

Modify the ImagePath entry to include the location of your configuration file like:
"E:\Program Files\mysql40\bin\mysqld-opt.exe" --defaults-file="C:\WINDOWS\my.ini" "MySql"
(please replace according to your particular program/file locations)

FYI my old entry looked like this:
"E:\Program Files\mysql40\bin\mysqld-opt.exe" MySQL