Thanks for all the replies! Seems mystery isn’t quite solved, but will certainly get myself a set of covers.

To address a few comments:

I’m 100kg/220lb, so heavier than many cyclists no doubt. I do tread lightly though and don’t drag my feet. When running you can’t hear me coming (except the laboured breathing!).

To my knowledge the cleats are genuine Shimano products. First set came with my new shoes and were fitted in the Giant store.

So will start with the clear covers and see if that solves the problem! Thanks again!