Interesting, we mill a lot of aluminium for our label application machines and never have this problem. So we can assume that it is the paper?
Our engineers never use paper to raise, or clamp surface protect and I never have a problem with their finishes, as I am the BOSS who has to be pleased before a machine leaves our factory. All our aluminium is anodised in either natural or red finish and again this always looks great.
If your milling the edges as you say and raising the piece to clear the bed the paper your using must be very thick to achieve this, so why not use another piece of plate to raise it?
Just a thought
Bri