I have a flight from MCO to BKK next week. I had to call to be added to the upgrade list. I was added to the leg coming from SFO to MCO on the way back. I could not be added to the upgrade pending list on the way to Bangkok because I have the same flight number from Orlando to Tokyo 0803 with a plane change at IAD. Even though you can upgrade the domestic portion of an international itinerary ....
From United FAQS
"Will I be able to upgrade on the domestic portions of an international ticket?
Yes. We’ll automatically request an upgrade on behalf of all elite members for any eligible United® or United Express® flights within the continental United States, Hawaii, Alaska, Canada, Mexico, the Caribbean and Central America, even if the elite member has international flights in their reservation."
Fell through the cracks on that one I guess!
Jim
FAQ may have been updated since you posted this but...
For flights that stop en route (and continue on with the same flight number), the upgrade is only permitted when upgraded seating is available and confirmed on all portions of the flight.
http://www.united.com/page/article/1,,50027,00.html
I know this because I am in the same boat for tomorrow. My company's TA booked me on a flight with a stop instead of booking connecting flights.