Snowdog, if I read your posts correctly, I think I know why your new rails cracked so quickly and it's not the suspension's fault. It sounds like the dealer never added the '06 reinforcement plates when he replaced your rails.
Do you have two plates bolted to each side of each rail near the rear bump stop where these cracks are? Since you mention you can see the holes in the rails it sounds like (and I am assuming here) there are no reinforcement plates installed.
If that's the case, I am guessing two things happened:
1. The dlr installed '06 rails which come pre-drilled with holes for the reinforcement plates and...
2. The dlr didn't install the reinforcement plates.
Just my guess. But if those rails have holes and no plates that's your problem. Make sure the dealer adds the reinforcement plates this time. They're available in a kit from Yamaha so he doesn't have to look up and order all the individual parts (plates, bolts, nuts, rivets, etc). If he doesn't know about the kit ask him to call Yamaha.
If the reinforcement plates are already there then my guess is wrong and you have a different issue.