Ordnance Window for Weapon Bay doesn't work from Captain's Chair

[Deantwo]

I had a variety of missiles (no rockets though) in my hold but could not see them in the F5 ordnance tab at the command station

Does your ship have multiple weapon/harvester bays? Which bay did you have selected on the command chair's fire control console?
The fire control console at the command chair has the added bonus of allowing you to access all the bays. I believe it is somehow random which bay is selected when you pull up the fire control console on the command chair.