Ive never seen it either. Are you using the MPCC with the 40d?
I don't worry about the mirror clips when i collminate all i do is use my laser collminator i made to get the angle of the secondary right. eg laser spot pointing to the middle of the primary, and then use the cheshire to get the rotation of the secondary right and the collmination of the secondary to the primary correct.
Apart from that im not sure whats causing your 3 difractions. when you look visually do you see them then? on a bright star i can see the diffraction spikes clearly. have a look at that and see if you still have them then, if so then its something to do with your telescope setup. ide offer to help but i no longer live in good old darwin towne!
and i don't know of many people up there, but i know for a fact that there is a small astro community up there. see if you can hook into them?.