Even after I figured this out I couldn't find Apple's documentation on this. (Yeah, worrisome.)
I first noticed a problem after attempts to run VirtualBox on my 128GB SSD MacBook Air. We first tried a Win7 .vbox and ran into some network issues, then I tried a smaller sized XP .vhd image. The latter worked, though getting VirtualBox to use the .vhd was a bit odd; I think I did better ignoring the few web references I could find and simply telling VB to create a new XP image then selecting the .VHD when asked for drive.
After that process I checked available disk space, and the Finder said I had a 120GB drive with 228GB available.
So I ran Disk Utility and found I had about 58GB free but my drive was corrupted due to "incorrect number of file hard links". DU told me to boot into the ML Recovery Partition and run Disk Repair.
When I did that though, my OS drive appeared grayed out. I could see other non-gray items I could "repair" but that did nothing.
So why was it grayed out?
My guess was encryption. Even so, Google was no help. I did see that the Disk Utility toolbar had a new icon however, one called, I think, Unlock. I clicked on it and was invited to enter a password -- but not, curiously, a user name. I entered my admin pw and that worked. (This smells like a security hole btw -- not asking the un is weird. I suspect I could have turned off File Vault encryption first and avoided this mystery.)
After I did that my system drive was no longer grayed out. I ran Disk Utility repair and it said the drive was better; I ran verification twice to check.
On restart, however the Finder still has the wrong amount of Free Space -- though now Disk Utility says the drive is fine.
So I'm not entirely happy. But at least I've documented how Disk Utility Unlock works from the recovery partition.
Update: The VirtualBox VHD thinks it has a 127GB hard drive. Disk Utility says I have 69GB free. I'm suspicious that a hard link in the Virtual Box is messing up the Finder, but I can't find anything on this...