Lots of times we get worried because of one problematic system but we forget that disorders usually cause 'packages' of symptoms.

For instance, a heart attack  in men is usually accompanied not just with chest pain but with lightedness, sweating, nausea, pallor etc. as well.  In the same way, meningitis usually comes with a stiff neck and things like headache, fever, vomiting, sensitivity to light, etc.

Many of our symptoms that seem purely muscular in nature; ie involve pain in the muscles are, in fact, due to muscle strains we don't know we have and they usually resolve themselves in a week or two. Of course, only a doctor has the skill and experience to diagnose you correctly...and if you have pain that does not go away in a relatively short period of time - as you are having - you should see a doctor. 

Good luck!