A few things to consider and as you are wondering it could just be the saddle is defective but could also be: (as already mentioned) Different leg length (you mentioned this has never been suspect but hard to know for sure), Saddle height to high or too low, saddle is too far back or forward, since you have non-clip in pedals there's not likely a problem with foot position being wrong but if your feet are too close or far apart from each other it could cause knee problems, pedaling too slow of a cadence which can tear up knees for some people especially when climbing, even having the wrong bar position can be a problem (too high/low, too far forward/rearward). The saddle may be fine and being a Brooks tends to shape itself to your riding movements which can give you clue as to whats wrong. You might want to consider taking a few days off and let your knees recover since for some conditions the more you ride the worse it gets and can take months to fully recover if it gets bad enough.