K.M.
My husband is a PT and read this in a pediatric physical therapy book (of course he read it AFTER our son grew out of his colic stage!) and it said that some times infants get the vertebra in the neck pinched or kinked and it causes intermittent pain that is confused with colic. It is usually not ever diagnosed because #1 a baby can't tell you their neck hurts and #2 it is confused with colic and sometimes (and in your case too I'm guessing) parents are told to just "wait it out".
The cure is simple and just is adjustments and exercises for your infant.
I would suggest trying to see a pediatric PT, but make sure it is one who is experienced with young children.
It is worth a shot I would think...