Bah! I’ve been searching for help on this in these forums and online and as soon as I post a help request one here, I figure it out.
I can’t believe I didn’t think of it but then again, thats how most problems are.
In case anyone has the same issue:
I created my timelines in Premiere by quickly taking my HDSLR footage and dragging it to the ‘New Item‘ icon in the Project tab. This will create a sequence with all the appropriate settings for you footage. Apparently the cameras files have strange audio settings and any audio not from the camera will sound quite poor. For lack of a better explanation, the audio I was adding was ‘too good’.
The fix; I just created an HDSLR sequence using Premieres default settings.