While the Continental/United integration process remains a work in progress, one benefit that we saw almost immediately after the merger was reciprocal upgrades on the two carriers. But based on what happened to me today, this technology has not been perfected and it would benefit you to keep a close watch on your itineraries, especially those tickets booked on Continental with flights on United.
My ticket from Frankfurt to Houston via Washington Dulles tonight was issued by Continental but included two UA-operated flights. Theoretically, elite upgrades are assigned automatically based on FFP status and availability in the days leading up to the flight. Today, however, when I checked in for my flight I saw that no upgrade had been requested on my IAD-IAH flight. With a flight time of nearly 3.5 hours and first class now zeroed out, I was not pleased.
I am on the waitlist now and we will see if there are any no-shows (this is a United Express flight operated by a CR7 with six first class seats).
Sadly, I cannot point to an easy fix or way to remedy this problem. Perhaps it was because I was on an international itinerary where the transatlantic flights were not eligible for upgrades. There simply is not a lot of transparency right now in terms of how upgrades are assigned. In any case, my only advice is to monitor NF space and give UA a call if it seems like you should have been upgraded but you have not.