Just swapped to a ship I haven't used for a month or two.
- The fire groups are empty.
- There are 3 blank columns in the fire groups A, B & +
- I can move the cursor freely around the blank columns.
- No issues with setting weapons and scanners into groups (other than not being sure I have them how they were)
- The fire groups remained as set above after exiting to the desktop and restarting.
So my only issue seems to be the wiping of the fire groups, I did have a management issue with my Scorpion on day 1 but that went away after logging to main menu.
I don't intend to visit all my ships to reset their fire groups until I need to use that ship in a vain bit of wishful thinking that the settings will miraculously return.