Possibly-spurious 'not uptodate. Cannot merge'

Recently (as of perhaps git 1.5.4?), whenever I update my l-k tree I get this:

loki 504 /usr/packages/linux/linux% git pull
remote: Counting objects: 638, done.
remote: Compressing objects: 100% (86/86), done.
remote: Total 517 (delta 430), reused 516 (delta 430)
Receiving objects: 100% (517/517), 74.91 KiB, done.
Resolving deltas: 100% (430/430), completed with 120 local objects.
From git://git.kernel.org/pub/scm/linux/kernel/git/stable/linux-2.6.27.y
   078bb16..5defaf8  master     -> 2.6.27-stable/master
 * [new tag]         v2.6.27.9  -> v2.6.27.9
error: Entry 'Makefile' not uptodate. Cannot merge.
fatal: merging of trees 34f70ec1fadcaad7de6979491e2dea9da735e6f9 and ded3f44559ce050e0ef014ebce093c5d9295ede8 failed
Merge with strategy recursive failed.

In this situation, 'git diff' reports no changes at all, but 'git reset --hard' gets the tree back into a state where merging succeeds, as does 'git update-index --refresh'.

I suspect the 'problem' is that I've hardlinked a bunch of build trees to this tree in the interim via 'cp -al', then applied patches to each of those trees with quilt, then deleted all those trees prior to the git pull. This doesn't change the original files at all, but *does* update their link count: is git getting annoyed by the corresponding change in ctime? (If so, why did it start happening only fairly recently?)