Ok, I'm going to try this.
EDIT: Giving it a clean was a good idea. The DVD drive was having trouble reading discs, now it reads them fine. But still got the noise. I had a closer inspection while the cover was off and the mac mini and put in a disc. Pressing the drive in certain corners makes the noise go away or reduce.
I've come to the conclusion that while Apple make great computers, Pioneer let them down with really cheap drives that warp! yes warp. Due to the tight tolerances, that scraping noise is just always going to be an issue with these drives. I bent the cover a little and improved the loading and on some discs now the noise has gone away, but not all. It's not as good as when I first bought it, but at least now I can read disc's noisily about 60% of the time rather than 100% of the time.
I'm suprised apple hasn't done something about this because it's still an issue on most mac's (probably a money spinner on warranties too).
Note: You'll notice that when loading the drive, the cover pushes up. That's because the spindle comes up inside and as it does so it relies on the flimsy drive cover to push it onto the spindle. Imagine over time that cover being pushed up lots. After a while discs don't get onto the spindle all the way which is what I think is happening. i.e. it leads to discs going out of balance a bit and also the laser being a little further from the disc giving read problems. That's my theory anyway. After pushing the cover down a little and cleaning the lens I'm not getting those problems anywhere like I was.