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Hmm actually I always thought it is the other way, that clipless means higher seatpost.
I'll try raising it as you suggest next ride.
This would mean my seat height was also not optimal when riding clipless then right? But maybe not enough that is causing any pain or discomfort.So there is a difference between the optimal seat height for the two side of the pedal.
Hence to me it defeat the purpose of two type on one pedal.
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Yeah, hence my "Could it be that your position to begin with was wrong?" question. You may have just been masking an issue with it being "close enough" to not give you pain, but then moving even further away from optimal with flats caused the issues.
Those clipless+flat pedals are for commuter types or ride to the shops types. I'd never ride any distance on the 'other' side without adjustment, ie. set them up for what you normally ride (say clipless) and then just do short stuff on the flats like nipping to the shops.
If you're gonna ride far in flats, use dedicated flat pedals or adjust saddle (up) like I said and don't forget kids, #hippyisalwaysright ;)
Anterior knee pain is usually from the saddle being too low.
Hence my point about needing the raise the saddle when you move to flats (because you've effectively shortened the distance your leg travels with the higher pedal+shoe stack).