I also have X-Fi elite pro and remote does NOT work in Windows 7 x64 Ultimate, however receiving LED flashes on the external box, same as your case.
I installed both drivers and console launcher, because i like to tweak the equalizer, which i can do only thru CSL.
Idea came to my mind though, to turn off user account control, to see if by any chance administrative rights were required to operate these controls thru remote. As it turns out - no. Then i remembered that i can push these knobs to turn on/off e.g. Crystallizer and they DO work, so now i think it's something with remote support on Windows 7 x64. Tomorrow i'll try to install Vista ultimate 64, and then xp64, just to see if it works on these systems.
If by any chance you'll somehow get it working, please leave me a pm or something with explanation how you did it.