Finding fare differences between the PC version and the web version seems to be pretty common on international itineraries, especially those with open jaws.

I spent last evening planning a trip in May.
05/12 JFK LAX UA
05/15 LAX SYD UA
05/26 SYD SIN QF, BA, AN, or SQ
05/29 SIN HKG UA
05/31 HKG JFK UA

The web version reported some astronomical price above $3500. The fare shopper on the PC version reported $3000 when I turn off the preferred airline option OR (have it on with only UA as the preferred). I even called UA Intl Reservation 3 times and they all told me the lowest they can do is $3000.

However, when I went back to the PC versionand specified UA and either QF, BA, AN, or SQ as the preferred airline, the fare came out to $2057. It seems that the reservation center couldn't see the $2057 BLSXP fare.

$3500 vs $2057 for the same exact flights!!! UA Connection has potential to be good but I find it amusing that I have to do some weird tweaking to get the lowest fare.

Good thing about my trip is that all segments are booked in B. Upgradeable at only 25,000 round trip instead of 50,000.