Hi Stephen,
I ran into this myself and gave it a shot at solving it. I've uploaded a video if you want to check it out
https://www.youtube.com/watch?v=L3ASxYG34tQ&feature=youtu.be Please note though that I'm still learning how to do this stuff myself so while it does appear to be working, I haven't yet tried mirroring it or seeing if it messes up the matching that's set up later on. As far as I can tell though it should work reliably (for those who checked out the video, if you see any potential problems with the solution I came up with I'd be very grateful if you could let me know about them!), and I plan on using it for my own rigs. Also if you're interested in why this may be happening, take a look at the videos listed below
https://www.youtube.com/watch?v=P8xmfDI1pUI - A really good lecture about aim constraints that explained why things flip (like the shoulder control does) and how you can use an aim constraint to fix this
https://www.youtube.com/watch?v=KYY7qo0z5h8 - An example of using the aim constraint to rig a forearm twist to solve popping that you would normally get there also