Thanks for everyone's comments - I finally found where the large chunk of client time was going. Client runs are still slow, but 5 mins is a lot better than 20 minutes. The issue in our case was having the directory that contained the nagios config files managed by puppet (purge => true, recurse => true, force => true), but also had a source set pushing some real files as well as the files in the stored config. The process of merging those together seems to have taken about 12 minutes in our case.
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