Sometimes I fly the miners to a location, and they produce. Sometimes they don't. Is there something fishy going on thats preventing me from mining? Can my ships mine above a civilian mining center?
Yes, they can mine above a civilian mining post.
I had the same problems in 5. 20. When your mining fleet arrives at the asteroid, just check your colony in the F2 economic windows.
In the mining panel, the very first line gives a sum up of how many ground based mines and how many orbital mines are present and working.
If your mining fleet arrived and there are no orbital modules, then you may have a problem.
Sometimes, it's only a matter of refresh. Close and reopen the window, or just select your playing race at the top of the F2 window : it will refresh and your orbital modules may appear.
If they are still not working, go to the task force window (F12) and give the order to your fleet to go to the colony, as if it wasn't there already.
It has always solved the problem for me.
If your orbital modules are well listed and you still don't have production, then you have a problem I don't know.
Hope that helps.