This bug seems to be somewhat reproducible:

  1. Set up ~/annex using webapp, keep empty.
  2. Add another local repo, eg /tmp/annex, and combine the 2 repositories.

Now files written to ~/annex should quickly appear in /tmp/annex, and vice-versa. However, this seems not to happen at first. There's a pause for some reason until changes start propigating. Apparently a push from the repo that got the file to the other repo doesn't happen. After this pause, syncing of changes starts happening quickly, as expected.