Another potential bug. In the ships.tbl entry for the EA Omega, you added the "no replace" flag to the 4 engines subsystems:
$Subsystem: engine01a, 3.5, 0.0
$Alt Subsystem Name: Engine01
$Engine Wash: LargeWash2
$Flags: ( "carry no damage" "no replace" )
$Subsystem: engine02a, 3.5, 0.0
$Alt Subsystem Name: Engine02
$Engine Wash: LargeWash2
$Flags: ( "carry no damage" "no replace" )
$Subsystem: engine03a, 3.5, 0.0
$Alt Subsystem Name: Engine03
$Engine Wash: LargeWash2
$Flags: ( "carry no damage" "no replace" )
$Subsystem: engine04a, 3.5, 0.0
$Alt Subsystem Name: Engine04
$Engine Wash: LargeWash2
$Flags: ( "carry no damage" "no replace" )
This results in the engine submodels disappearing once destroyed, even though you added "engine01-destroyed" submodels to the POF?
Also, the "fire down normals" flag is making some multipart turrets to fire shots at empty space, for example on the Primus or Warlock.