Sometimes gate agents just make mistakes or just don't care.
I know one time in November, I was commuting home and there were seats available in FC on a fNWA flight (I work for Comair). I was using my pass privilages and I was assigned a seat in coach, after I boarded 3 jumpseaters (I assume they were jumpseaters as I saw them at the gate talking to the gate agent) 2 Jetblue and 1 AA, boarded and sat in FC.
I wasn't really happy to see that, coach was wide open and since I was in uniform I wouldn't be fully able enjoy FC. So I let it go as it wasn't a big deal, I had a seat home and that is all I really cared about.
I also watched a DTW gate agent clear all off line JS'ers before Nonrevs on a DCI flight. (even the 2 of us pilots who were using our pass privelages to commute). When I looked at Travlnet (godbless the Iphone), he had coded the 4 Js'ers as UP4's or soemthing like that (showed that they were standby upgrades, usually if you already have a ticket in coach, I knew one of the guys JS'ing and he did not have a ps ticket). This put them above every non-rev on the list. Luckily everyone got on, because I'm not sure what we could have done (I guess I would have jumpseated to get to the head of the line).
That being said those are the only two instances I have had (or recall) in the last 5 years and they both happened in the past 7 months, so they very well maybe merger related growing pains.
And another question, Are the agents in SYD Delta employees or outsourced (swissport or something like that)? The reason I ask is sometimes the outsourced agents work 10 different airlines and maybe they got the policies confused.