I will make a guess E, and it is purely a guess (ie. no inside info.)
I will prelude this by saying I like Jones and value him a lot higher than some here do.
I reckon there are concerns about his coachability. The issue with Jones is that he hasn't really been able to find that niche between attack and defence. He has an attacking mindset and really only knows one way. When it comes off he looks great, breaks tackles, kicks a neat low pass into an attacking position. When it doesn't come off he gets caught or f**#s up a low percentage kick.
My guess is that the coaches have been trying to get him to temper his attacking nature a little, having failed they have given him a negating role to really drum in the defensive mindset.
I hope we keep him, he is a strong, talented, durable player with good skills (contrary to what some believe). If thinks click he will be a mainstay of a midfield, hopefully ours.
NB. I was exactly the same as Jones as a colt.