I know this crowd likes their swept-back bars so I thought you could help. I'm also going to ask my bike-fitter about this next week.
I was running drop bars on my Salsa Fargo and had the saddle set at a certain height and set back. I never experienced any knee pain. I switched to a VO Crazy Bar, with a longer stem, and despite being quite comfortable through my upper body, and having better handling on my local trails, I've now developed pain on the front of one knee. I did not adjust the saddle.
I know that one factor was the increased weight on the saddle from being more upright has led to my seat post slipping a couple of times. I've caught this mid-ride, twice (and I've checked in all 10 or so rides since switching bars). So I've ridden at least part of a ride (maybe 20-30 minutes) with a seat post that was about 2mm lower than when I started. Not much, but I'm super-sensitive to fit.
So my question is whether one should adjust their saddle height and set back when riding in a more upright position (like 15 degrees more upright, give-or-take)? I wouldn't have thought so, but other than going back to drop bars it's the only thing that may resolve this. I ride this and my Riv on a regular rotation, and never have the pain with the Riv, on or 1-2 days after riding. With the Fargo, it feels strange on the ride, and I definitely feel it later that day and next day.