Do you have any pictures of the problem? Does the saddle appear to be properly placed, but the string is not properly spaced?
I'll share a little story - Shortly after getting my latest bass, I thought I had a problem with the string spacing on the G string just by looking at it relative to the other strings and at how it aligned over the fret board... I lived with it for weeks and would scratch my head and kick rocks over it every now and then... It turned out that the string actually was just simply not in the slot.

Yes, I'm embarrassed to even tell that story. In my defense, this was right after the first time I changed strings and I was not yet familiar with the bridge, and the slots on this BA II are not very deep... but, that's all it was - So learn from my mistake and make sure that the string is seated in the slot.