Running and injuries

Right, I've got the trainers now and I've stretched and warmed up well. But my legs are still killing me. Years ago I had a scan on my legs as my spine is crooked. That showed my knees, ankles and hips are slightly disaligned (sp?) I wondering if the pain is due to that. Would I be best going to the docs? It's my lower calves and ankles mainly, feels like it's burning when I'm running and after it feels like they are seizing up. Anyone have any experience of this? Thanks.