Yes, I recently had the same frustrations trying to book not-too-complicated NYC-AVL-BOS and PDX-NYC-AVL-PDX itineraries, having first identified the options of choice (involving both UA and US flights) on ITA. No amount of manual forcing of connections in the "multicity" function on the UA site would replicate my ITA selection, with the identified fare classes.

My diagnosis of this experience was that (i) (most importantly) the website was suppressing all US flights without a UA codeshare, and (ii) the fare class search function on the website is clunky anyway, even when just searching purely UA metal. And the most frustrating part of the experience was that the UA engine has no way of specifying "I really mean this departure time"; each segment comes up with a large number of irrelevant departure time choices, and on re-searching, the specified departure time gets removed from the previous specification.

In the end, I had to book my preferred options on Orbitz, thereby incurring service fees/commission charges for both the passenger and the airline. UA's greed in trying to suppress competitive (but still *A) options from the website offerings seems to me to be of very dubious financial advantage to the airline.

In my book, the ideal airline website (from the passenger's viewpoint) would be able to input an ITA Matrix itinerary. But given the airlines' blinkered thinking about biasing their booking engines, I'm not holding my breath expecting this any time soon!