I'm having the same problem with my current build. I got an older, unused Dura-Ace BB that had a 103mm spindle and am trying to use it with the Sugino Messenger (RD's with an 1/8" specific chainring) and my chainline is also off by about 4.5mm.
At first I thought that the spindle length must have been wrong, but it's definitely a 103.
I don't know what to do.