The query is running dramatically slower than the MyISAM query, sometimes even causing mysql to freeze for a while. I searched this list and found a few people saying that on FreeBSD mysql should be compiled using linux pthreads if you are using InnoDB or else I would get this exact problem. Has this been resolved or is should I recompile? I am using native freebsd threads.
Compare the output of EXPLAIN for both MyISAM and InnoDB. Also, if you have a Linux or even Windows system around, test the same query on them to see if there is any difference.
I am not that familiar with FreeBSD, but from what I've seen, I would tend to use the approach "when in doubt, use LinuxThreads". The advice you've got does make sense - InnoDB runs a number of background threads, so if your thread implementation is lacking, it would hurt InnoDB more than MyISAM.
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