I think I'm using all the same versions as you. Everything is up to date, and I've been having this problem for several months now across a few versions.. Also driving the wife nuts! Sometimes I'll find switching tuners works ( I've got an Eyetv diversity and a soft button on my harmony programmed to do that) but mostly it doesn't help.

I have a suspicion that it may have something to do with Mavericks or yosemite. I took a long time to update to Mavericks because everything was worki so well, I didn't want to mess it up. Pretty sure this started happening after upgrading to that. Yosemite was out not much after that, so I did a clean install of yosemite and all my apps, only to find it's still happening.