The companion may only be confirmed on the day of departure at the airport within two (2) hours of the flight.
http://www.continental.com/web/en-US.../upgrades.aspx
So the OP's question is moot, BUT what the heck was the companion doing as #1 on the upgrade list > 3 hours out if there were in fact higher-level elites (Plats and/or Golds who paid higher fares, as evidenced by the fact that they were upgraded) on the list?
I guess it's possible that the companion was mistakenly put on the list by an agent and therefore popped up to #1 on the upgrade standby list, but then the 3-hour EUA ran according to the rules.