Prior has been diagnosed with a "loose shoulder", which is said to be a genetic thing and fixable. He has been working out on a program that specifically targets his shoulder to try and correct the problem.
This is a quote from the cubs site.
I've heard a lot of speculation about the starting rotation for next season and was wondering what Mark Prior's status is? Will he be healthy and ready to start the 2007 season?
-- Brian K., Iowa City, Iowa
That's the plan. Prior is working with a specialist in San Diego six days a week, strengthening his right shoulder. But it's December, and the Cubs won't know for sure how Prior is until he gets on the mound in Mesa, Ariz., in February.