My advice would be to see a physiotherapist.

Get them to assess the area and they will likely do some soft tissue massage through there and other treatments depending what they find.

It could be one of many things, the fact that it prevents you from running for months suggests that it is not of muscular origin (unless its compartment syndrome)

It is also possible to have fibular stress fractures, its really difficult to tell from your description. Trial 6 weeks of physio, if its not getting better go see a sports physician or get an Wikipedia reference-linkMRI scan.

It could even be referred from the lumbar spine.