Misterious warning about file system boundaries

Heya,

now what is going on here? After upgrading to current next I get

warning: working tree spans across filesystems but
GIT_DISCOVERY_ACROSS_FILESYSTEM is not set.

in several repos, such as my local git.git repo. That is certainly on a
single file system only (ext4 over lvm over luks, all on one partition,
Fedora 13). I also get this for another repo, but not for every repo. It
goes away when I set the var and comes back when I don't set it, of course.

Although I haven't bisected this should be due to
52b98a7 (write-index: check and warn when worktree crosses a filesystem
boundary, 2010-04-04).

How does the code detect a file system boundary, and where could it go
wrong?

Michael