This has occured to me on numerous trips to/from the USA. Last time it occurred I spend the time to interrogate the UA representative I was talking to (I have a VOIP phone for the USA, so its a free call for me), having lived there for so long.
Anyway, she told me that there is a software bug in the upgrade system, that everynow and then, and she had no definitive reason for it, on a change of plane type i.e. 747 to 777 on an upgrade request, the first request will go through, but all subsequent requests are left in Waitlisted status!!
Given that there are change of planes in LAX in almost every case (sometimes Dulles flights are 747's), this has resulted in MANY of my second/third legs not being upgraded until CheckIn!! And then, on busy legs, such as Chicago or Denver, no upgrade at all!
She indicated that the solution was to book each leg as an individual legs i.e. book MEL to LAX, then LAX to DEN then DEN-BOS or whatever, whereas the booking from MEL-BOS would have the bug trigger!
Anyway, that is what I was told, whether or not its true............
But, being a programmer myself, it would not surprise me that such a bug may in fact exist!