Totally agree to go see a physio as they will help with this problem and will give you specific stretches for your preferred exercise to prevent problems later too. I had shin splints from jogging even though I was wearing proper jogging shoes, but it turned out that I had flattened feet and needed insoles. I also had other foot problems that this sorted out. You could need the same thing and if you have incorrect foot position you will also get more knee, ankle problems etc as the whole alignment is out.
Hope this helps. Good luck with the physio!