Just to chime in here and give some input:
I had this issue appearing on my machine as well and it only happened when editing files on a mounted drive located in a VirtualBox guest (Debian fwiw). I had other issues with that setup (file name case sensitivity, versioning also locking up, filesystem watchers not working and what not) that led me to reversing the setup. I now have the projects located on my MacBook and the VirtualBox guest mounts these instead. Cured all of my problems.
And to maybe spare you from digging further into it, this didn't just happen with TextMate. I tried other editors as well, some of them didn't even show a notice that the save didn't go through and just silently went on. Re-openend the file and all changes were gone.
At times it helped touching the file directly on the guest system (via touch or a text editor), but it wasn't a sure fix.
I know it's not a solution to the problem at hand, but maybe sheds some light. Pretty sure these are issues within the mounting process.