I was shown how to improve poor intonation on wound strings this Saturday. I brought in my #2 guitar to have the intonation adjusted (as well as my #1 for the Plek job) and showed the repair man the poor 6th string intonation.
He took the guitar and pushed hard on the string right where it breaks over the saddle. Guess what happened! The sting was so close to being in tune again it was like watching a magic trick.
Appearantly, wound stings do not bend over the saddle edge very well and actually arc over the edge. When you push down on it, it makes the string contact the exact edge of the saddle. Before doing that it arcs over and ahead of the saddle point and will be sharp.
It you are having trouble with your wound strings having poor intonation, try it. The difference is dramatic.