Hi,
the most important changes between 1999/2006:
1) Nova Cannon is no longer guess range but makes use of a scatter dice.
2) Attack Craft limitation (one cannot have more attack craft active in play then available launch bays in his fleet (at that point in the game)).
sub 2) Ordnance no longers runs out when rolling a double on the Special Order to Reload Ordnance.
3) Some point changes: Retribution/Emperor swapped, Styx 275pts (260 in FAQ2010!).