I'm guessing that I have pretty much the same setup as yourself. I run a 2006 Mac Pro w/ Remote Buddy, an Apple Remote, and a Manta TR1 transceiver (purchased from Twisted Melon when I bought Mira, but now of course I don't use Mira anymore, so it's long since uninstalled). When I auto-updated OS X Snow Leopard from 10.6.4 to 10.6.5 yesterday, Remote Buddy stopped recognizing my Manta TR1 transceiver. Like you, I checked the System Profiler, and the "eHome Infrared Transceiver" DOES appear under USB, so it IS recognized by the OS, and is getting power. I tried re-installing Mira, too, just to see if that still worked. Mira DOES seem to recognize the Manta (I did some USB plugging and unplugging, and watched it appear and disappear from the menu), but my Apple Remote doesn't seem to work through IT, either. So maybe it's not just Remote Buddy that's been crippled by this update.

I'm totally hooked on Remote Buddy. I use it for EyeTV, Boxee, and various other apps on my HDTV. I CAN'T LIVE WITHOUT IT!! :p That said, if anyone figures out a fix, please post it! Let me know if there are any other details I can provide about my version of the problem.

Thanks in advance!

Sincerely, 
Chapin Klein (loyal Remote Buddy user)