Not I solution, but I am hoping a similar issue to provide more insight. I am seeing your auto-connect issue, but I only seeing the issue on the first network listed in the preferred networks. I recently switched the order of of my preferred networks, and the auto-connect failure was immediately switched to the "new" first network.
To elaborate, I have never had issues with my home network. However, a few days ago I switched my home network to the top of my preferred networks list. Now I must always select my home network to connect. Also, I was always having problems with my parent's network, which was first in the preferred networks list. Now that it is second, I have no problems connecting to their network automatically, when waking from sleep or from a clean boot.
I am still searching for other similar reports of this issue.