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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.
Not sure I can describe it accurately, but there is some pain in the front part of the knee if riding with vans on the flat part of the pedal,
Pedals are the SH500 same as @chris0 up there.
No such pain when using the same pedal with clipless shoe (Shimano xc5) on the same seat height or when I was using MKS gamma before.