After searcing other message boards looking for a possible answer I was able to find a work-around to the shuffle problem with the iPhone/CX 5 combination.
In order to "reengage" the shuffle you need to switch to another option on the radio head (FM, AM, etc). Then manually press play on your iPhone, then press the shuffle option. Once you've started the music on your iPhone you can then switch back to bluetooth on the radio head.
If you're doing this when starting your car, be sure that your iPhone bluetooth connection has completed before starting this process. I've noticed that the shuffle will "disengage" again if you switch to any of the other options (FM, AM, CD, etc), this also includes if you get a phone call. If this happens you have to perform the above process again.
The system can be a little wonky sometimes and doesn't always take. On occassion it's taken me a few attempts but it works.
I hope this helps you all until an actual fix is found.