HDMI CeC is the solution that has been long sought after. It enables flawless one-remote operation of your system without any hiccups or bugs and without the need for those pesky high-dollar universal remote controls.
As you've seen, it doesn't actually work.
As a long time systems integrator of high end remotes (Crestron) I have come to one certain conclusion: The manufacturers don't give a damn about making things easy for consumers to use!
Sony, Samsung, Sharp, Pioneer, etc. Nobody wants to play well with others, and mixing and matching or even building a decent product across their own product line is basically unheard of. Philips, the originator of the famous Pronto remote control, builds TVs that you can't accurately turn on and off or switch inputs on correctly.
Manufacturers are completely clueless and have no interest in getting a clue.
Heck, try calling your cable company and asking them which hard drive you need to expand the storage space on your DVR!
Kind of a rant, but the fact that HDMI CeC is turned on, out of the box, for most products purchased is nothing but a disservices to consumers and I'm sorry that you have fallen victim to this very poorly thought out 'solution'.