Just got back to NYC--here's the deal (as official as it gets from CO these days)
basically, the newest EUA enhancement (the "hub supervisor" in IAH used that word at least a half dozen times) is that EUA plain doesn't work for direct flights yet.
On the first segment, you get the upgrade if you clear both segments, but can't be upgraded in advance or via the at the airport computer b/c the system doesn't recognize you as being on the segment that is the first half of the flight.
You can't even be listed for the second segment at this point. The old process of listing for the second half doesn't work anymore.
The great part of my flights today were that I was told by no less than 4 different CO employees that I was on a waitlist for a first class seat--once for the original waitlist in PHX, once when I "didn't clear" for the upgrade at the gate (as I watched a silver clear), a second time at the gate when the agent apologized and said he couldn't figure out who told me I was on a waitlist, but would call ahead to IAH to waitlist me there, and then finally at IAH when I was told I was being waitlisted for the IAH to LGA segment. The "hub supervisor" finally let me know that none of this had occurred.
I may have lost the battles on these flights, but I won the war--the IAH to LGA segment was oversold, so CO bumped me to the next LGA flight 55 minutes later, put me in first on the next flight, and gave me $300 in travel vouchers...