Probably some tendonitis there... likely aggravated by poor technique in either running and/or the frequency of squatting.
It would probably be a good idea to back off and do some some tissue work and possibly some heat there.
Also, maybe some isolation hamstring exercises for now once you back off so you can bring them back into balance. It's likely you may be doing your running/squatting with mostly quads which is throwing them for a loop with too much stress.
YOu got any vids of running or lifting form?