Hi Brett,
so far I can’t find any “mistakes” you could have done (wich is probably the reason why noone answers in this forum) so I have the feeling that your hardware -ergo your 60D- might not work 100% propperly…. did Canon or some Camera-Electrics-Crack test it sometime ? I hope I am wrong but with my 60D I have no sound issues – no matter if I use intern/ extern or “normal”/ML- Sound. I recorded a classic music concert in quite good quality (not even using ML by that time) and since some months I use a Rhode Video Mic and get much better results (also recording with a Tascam DR-40 if the sound needs to be much better then average).
Sorry I couldn’t really help but maybe you let Canon check your camera since this is quite some issue.