Knees feel like they need to click when cycling

Patient : When I use a bike at the gym or a real bike my knees feel like they need to click but they don't. I spoke to a personal trainer who said that it could be the seat wasn't raised enough so I put it higher but it still didn't really do anything (it helped a tiny bit) at the same time she assessed my posture and said that I had a little bit of lordosis. As well as this I am wearing orthotics in both shoes because I have flat feet which were causing my knees to protrude inwards. I was wondering if any of these things could be causing it? I will be seeing someone I know who is a trained physio so she can have a look but before I go I was wondering what it may be. Thanks!
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