The 64 bit Cubase and 32 bit Cubase are totally separate programs with their own settings. Have you checked that you are using the same buffer settings? For example, maybe you have the buffer setting very low on the 64 bit version and somewhat higher on the 32 bit version.
Check for other settings or preferences that are different between the 32 bit and 64 bit versions that might cause a difference in performance such as Steinberg Audio Power Scheme, etc.
HTH
J.L.