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@ewanmac and @The_Seldom_Killer.
If you often overtighten your laces, try tying them with your foot dorsiflexed (flexed upwards) as that position will probably be largest size around your foot. That way they should never be a point where the trainer pinches your foot whilst running...
Compare it to tying the laces with your foot in plantar flexion and you will probably notice them get very tight when you dorsiflex.Loop/lock lacing the top of your trainers gives an extra couple of passes of lace right at the top, which then doesn't stretch so much under load. So you dont need to tie them quite so tight to prevent the trainer slipping on your heel.
I get a very similar pain. I even got it last night. The main cause for me is doing up my laces too tight, especially at the top by the knot. My running shop, which includes a sports injuries clinic, does say that overtightening the laces is a major cause of the injuries that they deal with.