It is happening on multiple machines. I have also raised a PMR with IBM who are currently investigating.
Further research and experimentation suggests a correlation between the number of documents and/or attachments in the database and the slowness of the search. The applications that took seven minutes to process database.properties was on our dev/test server and contained over 700,000 documents with 12GB of attachments. The same search on a design elements only copy of this database searched database.properties almost instantly. The search however did still noticeably "pause" for almost a minute when processing a form that had several jar files embedded in it, leading us to think a problem with searching attachments.
IBM support are aware of this. It also potentially provides a work around for anyone experiencing this problem if you can setup your dev/test environment so you only do these kinds of searches on templates or versions of the database with little or no documents in them.