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I found out what's going wrong. I have several SVN repositories with relative paths for products and an all encompassing SVN repository. Smart commits cannot be enabled/disabled per repository and thus all smart commits are picked up twice. Once in the all encompassing SVN repository and once in the relative repository.
I voted on https://jira.atlassian.com/browse/FE-4301 : Ability to opt a single repository or #pattern out of smart commits
Which version of fisheye are you on?
This seems to be a bug on the old fisheye versions (earlier than 2.7.4) and was fixed in 2.7.4.
If you are on an earlier version, upgrade to 2.7.4 should fix your issue.
Have a look at the link below, this was discussed in answers before