Well I went to the physio and it turns out, contrary to my OP, that my gluteus medius is a bit shoot and pretty much every other muscle in my leg far too tight. I've got some stretches and exercises and my knees feel a bit better already, even though I have cycled every day since Sunday (don't worry, I'm going to take a rest tomorrow).
Only time will tell whether this will solve it, but feeling much more positive about it all now. Might even dig a bit deeper into my pocket and go back for another appointment as Nicole at Peleton Physio was great - highly recommended (let's just hope she doesn't frequent this site and read this)!