Do you mean their new 747-400's vs. the ones they took delivery of between 1994 and 1997 (the original six aircraft?)
I have flown Ruby Tuesday, Tinker Belle, and Lady Penelope and they are all fine aircraft. There was only a minor difference, in that Ruby Tuesday was a newer one, delivered in 1996 or 1997 and had a different entertainment system than the other two planes. Virgin has two entertainment platforms, Arcadia and Odyssey. Odyssey was the newer one and the PTV screens on Ruby Tuesday were bigger.
I flew Virgin on the following routes:
August 1998 LHR-JFK, VS 009 A340-300 Rainbow Lady
August 1998 JFK-LHR, VS 010, A340 Maiden Toulouse
Nov. 1998 LHR-JFK, VS 003 B744, Lady Penelope
Nov. 1998 JFK-LHR, VS 010 B744, Tinker Belle
April 1999 LHR-EWR, VS 001 B744, Ruby Tuesday
April 1999 JFK-LHR, VS 004 B744 Lady Penelope
August 1999 JFK-LHR, VS 26 A340 Lady in Red
August 1999 LHR-JFK, VS 9 B741 Spirit of Sir Freddie
May 2000 JFK-LHR, VS 10 A340, China Girl
All fabu flights.