Cleat induced soreness?

Recently I had to buy different cleats from usual because mine weren’t available ( keo cleats ).
I used to have the grey ones and had to buy black ones.

I also changed the position of the cleats a bit to relieve some knee discomfort. Which worked.

But now I have another problem.
When out of the saddle for some duration, or on long rides, i get some pain under my right foot, where the cleat sits.

What could be the cause ?
I’ve never had that type of pain before, and it seems weird it could be the position of the cleat or the different cleat that causes this.

My main suspect for now would be that my cheap Shimano RP1 shoes are tired ( i’ve used th a lot, around 15000km ) and getting less rigid maybe ?

Take out the insole of the shoe and feel with your fingers if the cleat screws are poking through, they might be too long.