If I might hazard an answer to whether one of your hives is nasty:
 You are correct in writing that alarm pheremone can get on your gloves.
If you're working one hive (the nice one) first, then that could account
for some of the "nasty" behavior.
 The other thing to keep in mind is that it would be important to
establish that other factors are not at work- try working the nasty hive
first. There could be a few things at work: maybe you're working the
smoker too much and you're blowing cool smoke on the first one, but hot
smoke on the second one. Maybe it's the pheremones, maybe by the time
you're done with an extensive manipulation you're sweaty.
 Given that you're probably looking in on your bees somewhat regularly,
I'd at least conduct a few controlled experiments before requeening the
"nasty" hive.
 Hope I haven't made too much of a fool of myself-
  Phil Wood
  Univ. of Missouri-Columbia