[[!comment format=mdwn
 username="joey"
 subject="""comment 2"""
 date="2016-04-04T19:24:08Z"
 content="""
Note that v6 mode is still considered experimental.

I know that I saw a problem like this, where git-annex was reading the
pointer file and didn't always get around to closing it before it tried to
replace it. I thought I fixed it back in February though -- but that fix
may have bit rotted; looking at the current code, I think it could leave
the file open until a GC pass, so if the GC doesn't always 
run in time, that could explain the reported indeterminacy.

Please paste the actual version of git-annex you're using,
"latest build from source" is a little bit vague.

Since you are building from source, you might try pulling;
I've made a change that may fix it again.
"""]]