I'm using the webapp on my two main computers with up-to-date Debian (one has testing and the other one sid) and I have consistency checks scheduled every day.

The problem is that almost every time the check runs I'm getting the "Attempting to repair" message and git-annex starts using 100% CPU for quite a while, but after it it seams to have done no change to the git tree or the files.

The two computers are never on at the same time, but they are constantly syncing files (through box.com), I don't now if downloading files while the check is in progress might have something to do.