I had this problem on my 6000 series too. It eventually wound up breaking the arm completely off one day, as I was backing the tractor up it fell, got lodged under the tractor and broke the 3 pt.
When they replaced it, I had the them realign it, and locktite everything. My personal experience with the cub is that everything comes loose and falls off. I would buy a big tube of locktite. Also, if the 5000 is like the 6000 it matters alot which way the pins are placed on the arms, as they will stick and possibly bend them.
Of course this is just one guys experience on one tractor, and may not be indicative of other models and other owners experiences.