Using the latest 2.6 build, I'm seeing the following error during the second load of the parse scripts.
<source lang="C++">
----------- parse scripts ----------
60 script files
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'harvester' ignored!
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'corrupter' ignored!
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'bomber' ignored!
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'carrier' ignored!
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'supply' ignored!
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'gunboat' ignored!
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'ripper' ignored!
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'mothership' ignored!
</source>
I added some quick and dirty debugging messages to the script.cpp program to see if I could see the problem.
<source lang="C++">
Com_ParseAircraftNames: Aircraft type ufoids, Name scout, Number: 10, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name fighter, Number: 11, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name harvester, Number: 12, Max: 12
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'harvester' ignored! NUM: 12 MAX: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name corrupter, Number: 12, Max: 12
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'corrupter' ignored! NUM: 12 MAX: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name bomber, Number: 12, Max: 12
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'bomber' ignored! NUM: 12 MAX: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name carrier, Number: 12, Max: 12
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'carrier' ignored! NUM: 12 MAX: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name supply, Number: 12, Max: 12
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'supply' ignored! NUM: 12 MAX: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name gunboat, Number: 12, Max: 12
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'gunboat' ignored! NUM: 12 MAX: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name ripper, Number: 12, Max: 12
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'ripper' ignored! NUM: 12 MAX: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name mothership, Number: 12, Max: 12
Com_ParseAircraftNames: Too many aircraft ids for type 'ufoids', 'mothership' ignored! NUM: 12 MAX: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name }, Number: 12, Max: 12
</source>
From that I can see that the counter is starting at 10, I double checked the first load parse scripts during the start up process and I see this in the log.
<source lang="C++">
----------- parse scripts ----------
60 script files
Com_ParseAircraftNames: Aircraft type ufoids, Name scout, Number: 0, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name fighter, Number: 1, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name harvester, Number: 2, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name corrupter, Number: 3, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name bomber, Number: 4, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name carrier, Number: 5, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name supply, Number: 6, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name gunboat, Number: 7, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name ripper, Number: 8, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name mothership, Number: 9, Max: 12
Com_ParseAircraftNames: Aircraft type ufoids, Name }, Number: 10, Max: 12
</source>
So what I suspect is happening is that we aren't clearing the ufoids counter out, during the second reload when we are loading the mod.