We have local instances of JIRA Agile and FishEye/Crucible. For our source code we have a single repository that hosts many projects. I initially setup FishEye with just a single repository and set relative paths in the FishEye configuration. This seems to mess up things because both FishEye and Crucible also watch the root level.
So I removed the single repository and replaced it with a relative repository per project. However this still does not fix the issue, some projects have unrelated commits in the source tab, other projects no commits.
