In Disk Utility, are you able to create a
File -> New -> Blank Disk Image
*with encryption* ? I believe that is similar to what File Vault does, which is to turn your user home folder into an encrypted disk image file and mount it as your home folder.
The only other suggestion I can think of is related to your free space remaining. Since this is a MacBook Air, the storage may be a bit limited already. Is there any way for you to temporarily off-load some of your data to increase the free space. My theory here is that although you may have more space than is required by your user home folder, it may be sufficiently fragmented into small pieces so that File Vault is unable to do what it needs to do.
If you have AppleCare, you may want to contact the formal tech support at Apple using the AppleCare phone number
(800) APL-CARE (800-275-2273)
You can also report this as a bug in Mac OS X, using the feedback page
http://www.apple.com/feedback/
(although that won't help with your immediate issue)