I found this thread by searching for "Can't create kext cache under / - owner not root"
OK so I had exactly the same expereince after doing an Erase Free Space:
Slow shutdown and console logs like " Can't create kext cache under / - owner not root "
My disk was in tip-top condition before the Erase, checked with Disk Utility, Drive Genius and Tech Tool Pro before and after. No problems picked up - just the usual multiple ("safe") permissions repairs (yawn).
I did note that when running Erase Free Space, Disk Utility creates a temporary file, which may suggest that something is being moved and perhaps this is where error creeps in. Other threads suggest this has been problematic for other reasons. Of course this is pure conjectire on my part
The Terminal commands offered as solutions worked for me, so I can only suggest that those insisting there must have been a problem before are mistaken.
However.
Shutdown time was not fully restored to fingerclick fast so I investigated further.
Turns out I had experimented with MacFUSE and NTFS-3G but not fully uninstalled the MacFuse Core (only removed the PrefPane). This was causing kext unloading issues at shutdown.
I got rid of the remnants manually but reinstalling the prefpane would also have offered an unistall function so it's really quite straighforward. Suddenly everything was superbly quick.
I also experiemented with MacFUSE but found that even slower to shutdown Snow Leopard.
So this could be multi-factorial - and if you have slow shutdown I suggest you remove any FUSE components you have installed and see what difference that makes.
FWIW I now mount my NTFS Bottcamp partition as writable only when needed using the quirky but totally functional NTFS Mounter at http://www.ntfsmounter.com/