I had the same problem with the flat-bar road shifter and front derailleur on my wife's old bike. I usually set up a front derailleur like this: shift to lowest gear, turn all barrel adjusters almost in, pull cable taught, attach cable to front derailleur bolt, and fine-tune with the barrel adjusters.
The problem I found is that it led to way too much cable tension. The FD would shift to the middle ring too soon--it would shift from using the half-shift trimming click. Then, when the shifter is put into the actual second gear spot, the chain then shifts to the outer ring. Then, when downshifting, it would always go back to the inner ring, even from the outer ring (because the shifter really thought it was in the middle ring).
The only way I could get around this is setting up the front derailleur so that there was a LOT of cable slack in the inner ring. But it was difficult because I had to find some seemingly arbitrary slackness (as opposed to just pulling it taught). It also rendered useless the trimming half-click (which just pulled the cable to about where it should have been starting anyway), but at least all the gears worked well.
I did find that using a regular drop-bar triple front derailleur (Sora, specifically) helped. There still had to be some slack in the cable, but not as much, so it was a little easier dialing it in.
Don't know if this is what's happening to you, but if your front shifter has a gear indicator, check where it goes for each gear and see if you're actually getting to the last position when in the outer ring. Also check if the shifter has the trimming half-shift going from first to second and determine if it is being used to move the chain a whole shift to the middle ring.
By the way, I'm assuming you're using flat-bar shifters with the FD. That FD is not supposed to be used with road shifters, like STI (though like I said before, for me, it didn't even work for its intended application).