Time stops when you enter port.
There is a base time penalty for entering port (for navigation and berthing etc).
If your hull is damaged, it will be auto-repaired and the time required is based on how much damage.
Repairing a subsystem takes the time indicated.
Loading and unloading weapons, Spec Ops also take time.
Note that loading Spec Ops also incurs a time penalty for unloading any other ordnance on board.
There should be no need to rush while in the port. You can read orders, set up tube loadouts and settings. Aside from the enter port and hull repair times (which are automatic), time will not progress unless you perform an action requiring time.
I just verified that the times for loading weapons are working as intended. However the display times by each weapon are not taking into account the difficulty level which is a bug to be fixed.
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