Based on my somewhat limited experience, I would say that there are always HDMI handshake issues.
I've seen the oft-mention work-around of sending the video via HDMI from a sat or cable box directly to the TV, and then a digital audio (coax or optical) from the box to the receiver. I haven't had to take that leap (yet) but there're times I've been tempted. And I would add that the only reason that work-around is an attractive option is because the satellite and cable boxes are outputting one of the lossy compressed audio formats (Dolby Digital 5.1). If they were outputting multi-channel lossless audio (such as Dolby TrueHD) then that work-around would become far less attractive.
HDMI handshaking issues have prevented me from being able to use HDMI control. Not much of a limitation, really, but why have HDMI control available when there are so many handshaking issues that the feature is essentially useless in at least a significant number of cases, if not the majority of cases? (That's a rhetorical question, I think I know the answer).