How long do you allow your chain of command to work an issue before you go over their head?

It depends on the situation of the Servicemember, but at least you give your Chain of Command the courtesy to be aware of the situation.  I seen many situations when they try to retaliate against the Servicemember and labeled a "troublemaker".

This one had too many variables for a simple answer, some issues can take quite a while to resolve. I would say that as long as the CoC is giving feedback on the progress (which they should do) let them continue to work it. If you get no feedback (and have asked for feedback) then I think it's time to take another route.

Like SSG Fleming said, it truly depends on the situation.  If I had a Soldier unexpectedly get a NPD on his LES, I just inform the CoC of the situation and took the Soldier directly to Finance, because that is what I would do if my pay was messed up.  If it is something simple that isn't an "emergency" then we did the paperwork and sent it up the chain.  It allows the system to do its job and also shows the Soldier that the system does work of taking care of business but I truly believe it depends on the situation.