Hi Bergstrom.
Just a thought, are you using single point or zone AF? In single point if the only af point is not coinciding with an AF assist spot then focus is doomed to fail, if you are using zone then at least one point should find an AF assist spot.
I suppose after time the LEDs that project the AF assist spots might get weak, or are you frequently using the flash in a dusty environment, perhaps the inside of the red cover is dusty?
I guess it is problems like this that keep mission critical (eg wedding) photographers using genuine Canon accessories, they cannot afford to be hit with problems like this!
I have a pair of these flashes and the YN-E3-RT to go with them, after a few months and even fewer uses I noticed that one of the led cover lenses (clear plastic over the blue connection status led) had vanished from one of the flashes, annoying but no big deal, it still works.
I hope you get to the bottom of your issue.
Cheers, Graham.