Having followed this thread for a while, I wanted to suggest something, and I apologize if it has been considered already.
For those of you who are having this issue, have you considered the possibility of a hardware problem? Yes, it seems like software/OS, but it's very possible that it's a hardware issue, maybe a flaky or intermittent one. You might want to take your machine in and have it looked at. Maybe replacing a network card, or something else, will help.
I bought an iMac 5K Retina a few months ago, and out of the box it acted very strangely -- something that seemed to be a software problem but clearly wasn't because it was a brand new machine. It took some convincing, because the problem was hard to reproduce in front of the service people, but I finally convinced them to replace the machine. The new iMac worked perfectly and I haven't looked back.
So, especially if you are under warranty, I'd bring it in and have it looked at. And, be persistent. Bring screen shots of the problem -- maybe even video -- in case they can't reproduce the problem at their location. This documentation is essential -- they can't just shrug their shoulders if you have pictures and video to show them of the problem. You may also want to consider bringing it to a local computer store that is Apple-authorized, particularly if you don't have luck with the "Geniuses". In the few times that I've had hardware problems in my 20+ years of owning Macs, it was the local store that went to bat for me with Apple and not the Apple Store.