Nick - daft (ish) statement but try and track down (by recomendation -look up your local running club and give them a call, see who they use?) a sports physio in your area i had the same issue as you (with physios..) struggled with my knees for years, 3 different physios, all pretty much prescribed stretches and worked my knees / ultrasound application stuff, never with much success.
Decided to give it 'one last try' and, fortunately for me got recommended to a guy called Paul (Edgerton Clinic in Huddersfield, just in case you are close).
He took one look at me, diagnosed the root cause of the issue (in your case it seems its your ankle), set about resolving it an lo - long story short, things are very much improved....
Oh, and he's an mtb'er as well
Best of luck getting sorted.