you might get better and morer responses if you mention which brake you're using.
maybe say how you got the caliper straight....

two things you might check.

1. is the wheel correctly mounted in the dropouts?
2. are all the disc bolts tightened equally?

***if you've got a BB5, the business card trick works great to
get the caliper parallel to the rotor***

http://www.ecovelo.info/2011/04/15/a...5-disc-brakes/