I'm in a similar situation. I have an AS award ticket using CX in February JFK-HKG-SIN-HKG-JFK. Using a previous example above, my passport shows as follows:

Surname: Smith
Given names: John Peter

The AS ticket shows as John Smith and that is what shows on the CX website when looking up the booking as well. I sent a twitter message to CX asking about the middle name and they stated that the ticket needs to match my passport exactly. Apparently they did put a note on my booking to mention my middle name. That is all they could do since it was ticketed with AS and they did say that they couldn't guarantee there won't be issues at check-in.

I then called AS. They said they don't put middle names on the ticket and they couldn't do anything for me there. I even asked if they could add my middle name to the first name field, but in order to do that I would have to cancel and rebook which would potentially risk me loosing the award space. They did say that they added my middle name (Peter) to the secure flight information. They said that that is what the airline looks at anyway and I would have no troubles. We'll see and I will keep monitoring this thread before my flight.