I have a Kestrel Talon, with an Ultegra Group. I know that Ultegra shifters are for both the triple chain rings and double chain rings. Earlier this year when my LBS replaced a defective Ritchey compact crank, it started to exhibit 3 shift positions, like you would expect for three rings.
Since then, I have recabled the bike, and replaced the Ritchey with a FSA compact crank, i still have the same problem. The only good thing is that it appears to give me a little extra trim when I'm about to crosschain.
Rans Enduro Sport, Hase Kettweisel Tandem, Merin Bear Valley beater bike
Try this: Completely disconnect your shift cable and count how many shifting clicks your shifters have. Mine, which are old enough to have both Flight deck buttons on the right shifter, have four.
On a double crankset they set up to provide two shift positions for each chainring. On a triple crankset, they give one granny shift position, two for the middle ring, and one for the big ring. No adjustment is required for the shifters. I'm pretty sure that's the wan that Shimano intended it because my Flight Deck computers give the correct gear display in all of the shift positions.