Strange merge conflicts against earlier merge.

We are working with a series of closely related heads, and merging among them. I am sometimes finding merge conflicts that I don't think I should be seeing. Assuming two branches, 'local' and 'remote', where local has with remote before (*), and I have no conflicting changes in local...

 1 - pull and merge from remote. The merge touches file A, B and C
 2 - on local, develop on unrelated files O,P,Q, commit
 3 - pull and merge from remote. The merge touches file B, C and D. I
am sometimes seeing conflicts on file B and C, which was never touched
on local.

* - In the case i have, the ancestry before the merge is a bit
convoluted. AFAIK, this shouldn't affect us going forward. Both
branches have a common ancestor, though, and are now merging often
from remote to local.

We are using cogito for this, although on step 3 I have also tested with git-merge.sh and I get the same result. It could still be a problem related to how the merge on step 1 is recording the merge.

For an example, clone http://locke.catalyst.net.nz/git/moodle.git#mdl-artena-tairawhiti and register also the http://locke.catalyst.net.nz/git/moodle.git#mdl-local branch. Create two heads:

 master: 214e6374d49e6d014f0ba6f159d585a3fe468909
 remote: 05059be73c9e09e22b98bc796be35c595e551ed6

On git-merge 'testing merge' master remote you'll see conflicts over mod/quiz/editlib.php -- doing the same with cg-merge gets an additional conflict on mod/quiz/export.php. Neither of those files were ever modified on local -- however, both merges brought in changes to the same lines of code.

I suspect this is because the merge itself is being considered a commit on the local branch. Fair enough -- git has no way of ensuring that I haven't slipped in a few changes of mine in the merge. OTOH, it's pretty unexpected to see this on files that are not one char different from the 'remote' branch. Am I doing something wrong?

cheers,

martin