Found 3 different references to engine subsystem...
In the POF constructor suite there are 2 references to engines, (special and engines), special also is used for all subsystems, sensors, radar, communication and weapons... And not to forget the ships table which makes the 3rd..
Also have noted that if the spelling is not the same in all 3 the engine subsystem will not show up in fred or the mission (examples) $engine, $engines or $engine01 have to be listed the same in all three
Just thought this imformation to be important, because if the engine subsystem is not present the ship can not be disabled without destroying the ship in question...
Hopes this may be of some help.
(edit) Where I stated engine01, this comment is used for mutiple engines engine02, engine03 and so on..