are they the Ultegra dual pivot brakes? the set screw on top of the middle piece of arm (hard to describe) will adjust the spring tension and help to center the brake arms. You can also take them loose and do the gross centering, retighten, and use the set screw to fine tune. Shimano's Euro site has much better tech info than the US site.

http://www.shimano-europe.com/cyclin...20%28EN%29.pdf

see step 4

hope this helps