CiviEvent registration being assigned to the the wrong participant
I guess you are getting bit confused with Event registration 
When an Event is created to accept multiple participant 

The first entered member is considered as the actual member register and he is the one who is charged for all the participant amount too (in respective of the member is new or existing) 

I have done the same example against http://d46.demo.civicrm.org against Version 4.6.4 which is working alright - i don't think this is an issue

if you are still getting issue with this let me know with some example - thanks