Ikytwtlya apologies if this has been mentioned before, but have you looked at your trainers?
If they are old they may be losing their support or if they are not they might not be suited to your gait
If they are new, perhaps get someone to run behind you and look at your ankles and knees to see if you are turning in or out slightly.
Otherwise, try lacing your trainers differently, google 'rabbits ear loop' for lacing, this gives lots of support around the ankle.
Also are you running on a road? The camber of the pavement or road can add pressure to the foot that is slightly lower - I run on my right side so my right leg often aches more from the pressure of the slope. Try running in the middle of the road where it is flatter.
Hope this helps, I am sure we can find a reason and don't let it deter you!
agressive thank you! I shall walk in on Friday with my head held high, I am no January blow in, I know what I am doing and what I can do! 
Your crossfit experience sounds terrifying I would have certainly closed the lift and legged it
you are a stronger woman than me..