I had a look at the game engine source code and I believe I have found the issue. The recent fix for Java bots introduced the JsonStringEnumConverter.
The enum used by the engine looks like this.
My enum was declared as follows, following the same conventions as the starter bot.
START_AFTERBURNER(3),
STOP_AFTERBURNER(4),
FIRE_TORPEDOES(5);
If I remove the underscore, it looks like the engine is able to map and execute the correct commands.