namlit,
I had a similar case where I was flying Newark to LA to Houston to Fort Lauderdale. Everything was Q class except for Houston to Fort Lauderdale (which was Y). The agent told me that even though the seats were available, the Q class segments overrides my Y class making me ineligible for the upgrade. I am not sure what all that means but she explained to me that if everything is ticketed together, the whole ticket is classified by the lowest class of service. Also, if I had broken the ticket, I would be able to get the upgrade but my overall cost would be more without a rt.
I am sure I have confused you but I think it makes since to me.
crju