Why new version is slower?

[yelliver]

When I play Naruto 4 (G4NJDA) on an old version R2195, it run with perfect speed but with the same config on R4525, it run very slowly. Because i haven't a VGA so I just want run game faster, even with low quality so I decide to play on older version of Dolphin. But when I try to run Mortal Kombat Deception, it crashes and run Dragon Ball Z Budokai 2, it can run but has problems with character model. So who can tell me whether I can run Naruto on R4525 with more FPS (it sounds foolish but I config as the guide: How to speed up game, it can not be faster, but why it can run faster on older version). If I only play Naruto, I will be satisfied with the old version R2195, but it can not run 2 game above
PS: sorry for my bad English
Core 2 Duo T6600 2.2GHz
DDRIII 2G-1066
VGA G110M 256MB

[Chaoscode]

better hardware support = slower emulation.