Why don't key mappings work in training?

Allegiance training missions intentionally load the default controls so all of the dialog matches the controls you are using. You can work around this by simply opening and closing the Map Keys and Controls menu:

• Open the Map Keys and Controls dialog:
  • Esc-->(G)ame Options-->Map Keys & (C)ontrols
• Save the settings by clicking "Accept" without changing anything.

This will apply your already-set key mappings to the current training mission.