Ankle aches with clipless pedals

Firstly thanks for people telling me to stick with clipless pedals as I am getting more used to them after around 10 attempts. The only thing is my right ankle aches a little when riding, the seat was a little low and I have adjusted that but still it aches. I moved the cleat a little more towards the ball of my big toe yesterday and maybe this helped and my ankle still ached because of past mistakes.
The question is what can cause this? The pedals have a lot of give so movement is fine.
Thanks
The question is what can cause this? The pedals have a lot of give so movement is fine.
Thanks
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The advice said: sit on a table with your legs hanging over the edge (not touching the floor), and look at the angle of your feet from the straight ahead.
Then adjust your cleats to give your shoes (and therefore feet!) the same sort of angle when clipped in.
I'm sure there will be much more advice along shortly, but I guess it makes sense that if you're 'forcing' your feet to an angle they do not normally hold, then you will be stressing your ankles.
And yes, the ball of your foot (the big toe bone/lump on the side defines this) should be in line with the pedal axle.
What do the bike shops do to get it right? One thing suggested is movng the cleat left or right as the only thing I have tried is backwards and forwards. Ill keep trying as I don't want to go back to normal pedals, but may have no choice as the rides have been short so far and I wanted to really test myself once the fitness improved.
As one person says here, both feet are not necessarily the same and you may need one toed out more than the other.