I still think it will effect it because without it the two screw pins that go through the pads will go in farther then they should and the threads on the screws will go through the threaded portion and contact the pads at the top, see what I mean. Honestly I'm not sure if that is the problem but I would guess it is unless I could see your caliper itself, I'll go check my caliper tommorrow, I really don't think that the area there is raised at all, it should sit flush over the entire C-shaped area and the top portion. You may just have a lot of grime built up in there, try cleaning it out really good.
Trikes
1984 Honda 200x, 1984 Honda 200m
Bikes
1995 Honda CR125R, 1985 Honda XL100 (gone), 1982 Kawisaki KZ550 LTD,
2001 Yamaha TT-R 125L, 1983 Honda XL185S (current project), 2001 Suzuki SV650S