Ah CIH...what fond memories do I have of that little virus. Back in highschool I passed a Diablo 2 CD infected with CIH to pretty much everyone who wanted it. My computer's BIOS was protected against overwritting (praise dell) but a lot of my classmates weren't so lucky....Ah the happy times
If a FGPA could have circuit modifications on the fly, then this would be an issue, although you would have to have a software component to deliver the payload.