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After doing all this I came to the sad conclusion that something is flawed about PT's DB schema itself or the parsing code is badly written.
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Never used PokerTracker so I really have no idea, but sounds like it's just horribly written code from what you're describing. However, PostgreSQL isn't the fastest SQL db around, so if PokerTracker doesn't rely on PostgreSQL and can accept any SQL database (w/o transactions), try
MySQL and see if that improves performance.