If you create System Plugin that should work only on front-end you have to check in your plugin if current page is front-end. You can do it using this function: JFactory::getApplication()->isSite()
or JFactory::getApplication()->isAdmin()
Example usage (I assume you use onAfterRender event):
function onAfterRender() {
// Exit if current page is from Administration panel
if( JFactory::getApplication()->isAdmin() ) return;
/* your plugin main code goes here*/
}
It will prevent your plugin from modifying administration panel output. If you already done it and it does check like it should to, there is no way that reason of your problems is that plugin.