Hello,
This problem is due to the following bug (which will be fixed soon).
http://bugs.mysql.com/bug.php?id=27535
In a nutshell, using double quotes surrounding the "--defaults-file=..." parameter when creating the service is what is causing MySQL Administrator to be unable to find the config file.
Until it is fixed, however, there are 2 work-arounds:
Soution #1:
Re-create the service without using quotes at all. This would mean that you would have to have a full path with no spaces (i.e., C:\mysql\). So, you may need to move your MySQL basedir (or at least the config file).
Solution #2 (which is documented in the above bug report):
You can open MySQL Administrator without logging into a MySQL server by holding Ctrl and pressing "Skip" (the label is "Cancel" unless you hold Ctrl).
Then, open the Configure Service tab, ensure that Config Filename is set appropriately, make some change (and undo it if you don't want to keep it) in order to enable the Apply Changes button. When you click Apply Changes, MySQL Administrator will modify the Windows service so in a way that it will be able to read later.
Alternatively, you can use the "sc" command-line tool to change the binary path for the service:
sc config MySQL binPath= "\"C:\Program Files\MySQL\MySQL Server 5.0\bin\mysqld-nt\" --defaults-file=\"C:\Program Files\MySQL\MySQL Server 5.0\my.ini\" MySQL"
I hope this helps.
Best regards