When trying to perform the jql query "fixVersion in unreleasedVersions()" on one of our Jira instances we get a ClauseTooComplexSearchException. The error message simply says "the following query was too complex to generate a query from: fixVersion in unreleasedVersions()". Running the search "fixVersion in releasedVersions()" however, works without any problems.
Also the search, "fixVersion in unreleasedVersions()", runs without any problems on our other nearly identically configured instances.
Sorry for the too late response, but I recently ran into the similar problem, and I found your question.
When I looked at Lucene API and after some googling I found this issue.
JQL has a limit of 1024 clauses, you can only get the expected results for <1024 rows. So, if you have more than 1024 fixVersions you may run into this problem.
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