I was just about to post back about your original javascript file. Everytime I have applied my own styles it has specified the starting preset and '(custom)' in the first and second lines:
// Custom configuration for iRite
FCKConfig.XMLFullName = 'Advanced Manager Enabled (custom)';
FCKConfig.XMLFileName = '(custom)';
I can't think why it wouldn't declare a 'Custom' set given that you had selected and added styles.
Weird. Glad you got it working.