Eeeeeekkkk, i never thought of a piston not being square to the pad surface. The disc dialed fine in the bike, which squares away the disc to hub mounting surface. The disc also dialed fine in the lathe. As i was saying to blah9, i am going to try a new set of pads to eliminate contamination. If that doesnt work, then it may come down to substitution of the callipers. They are both BM-446 Deore, so that shouldnt be a worry. I clean the disc with an acetone, even getting into the clearing holes and making sure they are all clean. The annoying thing is my son's bike has the same brakes albeit with a slightly different hole pattern, and they work perfectly, front and rear. I will keep plodding away on this issue. I'll post it if i find the cause
Apologies to the OP and forum for getting off topic, but the suggestions recieved will hopefully help to sort this issue.
: Update :
Fitted a new set of pads to the calliper today. With the old set, and new, side by side, one of the two old appeared quite dark, even after a deep cut with a file, into the material. I couldn't say for certain that its contamination, but it was only in one of the two old pads. Anyway, got the new pads hot with pedalling against the brake, and so far so good. No noise, and a rear brake that feels more effective than it was, previously. Here's hopeing....