Finally after many reads , I saw what you meant so change does not = 0 To =0 ..
This is working now ..
Begin Small Integer Compare : [docking] Equals 0
Begin Small Integer Compare : [flight] Equals 0
Begin Small Integer Compare : [cargo-scoop] Does Not Equal 0
Execute command, 'Retract scoop;Retract cargo scoop;Scoop up;Cargo scoop up;Close cargo bay;Close cargo bay doors (and wait until it completes)
Set small int (condition) [cargo-scoop] value to 0
Begin Small Integer Compare : [landing-gear] Does Not Equal 0
Execute command, 'Retract landing gear;Raise landing gear;Retract docking modules;Raise docking modules;Landing gear up;Docking gear up;Docking modules up' (and wait until it completes)
Set small int (condition) [landing-gear] value to 0
End Condition
End Condition
Execute command, '((Power to Flight))' (and wait until it completes) ......VA only fires this once now
Execute command, '((Afterburners))' (and wait until it completes)
Execute command, '((RS- Afterburners))' (and wait until it completes)
Set small int (condition) [flight] value to 1
End Condition
End Condition - Exit when condition met
Begin Small Integer Compare : [docking] Equals 1
End Condition - Exit when condition met