What graphics card is it? Are there any other applications that slow down when you run them, or is it just FFXI? When does the actual drop in FPS happen, when POL closes and FFXI opens, or when you actually log in with your character and all the models are loaded and displayed? I'm guessing its a hardware problem here, but if the same video card works on the other pc, then its hard to say whats causing the problem. Also, Are you sure all the hardware is compatible? Sometimes old components do not play nice with newer ones.
EDIT:
Tault_admin (!empty($user->lang['WROTE'])) ? $user->lang['WROTE'] : ucwords(strtolower(str_replace('_', ' ', 'WROTE'))):
Its vista aka the devils system. I cant believe they released it in the condition it was in.
Perhaps I'm wrong, but if I recall correctly once you update to the latest (vista) version, all those issues are resolved. I do agree that vista was released too early, but I think Microsoft wanted to get it out because it had already been delayed something like 3 or 4 years.