Based on my own testing, Find my Mac causes the problem after reboot some but not on all Macs. I see this on a mid-2012 MBA and mid-2011 iMac. Funny enough a early 2011 MBP seems to be able to run Find my Mac and not have the problem. I have not tested a late 2009 iMac or mid-2012 MP.
So far, each actual home directory remains with the proper permissions and I've got very little reason to tunnel from the root down to my home, the sidebar is faster.
All things considered, I see this as a low impact bug and many won't notice it at all. What do people really do via finder and /Users other than pass through on their way to something more interesting. If you do have a notebook and want Find my Mac (I do), then consider just ignoring this bug until it's fixed. Finder preferences allow you to have your home folder always one click away.