Listen to your body, and find a doctor who will listen to you!
if the problem wud have been muscle the the x-rays wud have shown it..
i think it cud be muscles that are making the sounds,but if the pain in there and its consistent the u shud definately consult a good docter.
if u are overweight that can also put pressure on ur ankle.
make sure before going for a bath massage ur ankle with old for 10 mins..
eat almonds and calcium related foods..
touch the place where u feel the pain,,if its hurting while touching then its muscle but if u dont feel pain while pressing then it cud be bone..
so i thinkif ur pain is regular and unbearale u shud see good docter..
Have you been on antibiotics in the last few months? Some antibiotics can cause the tendons or ankles to get very stiff. So stiff that if you step the wrong way, you can actually tear the tendons! happened to a friend of mine who was on Clindamyacin (spelling?). She got out of bed and broke her tendon by stepping down too hard....
Wishing you the best
Sorry to hear about your ankle, that sounds frustrating! My suggestion is to see a Orthopedic Doc (if you haven't). He/ She could properly read your MRI, which is where I think the answer lies. He/ She needs to do a "hands-on" evaluation also.
I am a Orthopedic Surgical First Assistant (25+ years) and I have assisted on thousands of ankle procedures. Also, you will probably get more responses in the Orthopedic Community (especially since I am the Leader of it ; ) )
Best wishes! JD1963