Apparently, when the textconv if configured in git client configuration (e.g. to show textual content diff between two Word documents), it may affect repository indexing. In particular, when text converter fails with error repository indexing can't continue, see https://answers.atlassian.com/questions/15300297/answers/15302217

Perhaps FishEye should globally apply --no-textconv option to git diff command to disable such extensions explicitly.