There are 2 my.ini files in play and there will always be a conflict with having 2 instances of MySQL.
(Why would you need 2 instances of MySQL)
Try uninstalling the stand alone version of MySQL you can then use the MySQL in XAMPP at the command prompt if you wish.
When you have uninstalled the stand alone version of MySQL do a file search and make sure that you only have one my.ini file, the one found in the \xampp\mysql\bin folder, delete any more you may come across - often a stand alone MySQL will put the my.ini file in the system path folder, C:\Windows for example.
If you use the XCPv3 (xampp-control-3-beta.exe) found in the xampp folder you will see an XAMPP-Shell button which will allow you to use the command prompt with the MySQL version in XAMPP with ease.
New users can find self help by reading these:readme_en.txt
file in the xampp folder.http://www.apachefriends.org/en/xampp-windows.htmlhttp://www.apachefriends.org/en/faq-xampp-windows.html
Some useful reading that may help you help us to find suitable solutions:viewtopic.php?f=16&t=48331viewtopic.php?f=16&t=32670