First, you probably want to mention which coin you're mining, it would definitely help w/ diagnosis.

Second, one thing to watch for is transactions getting forked out of existence.  I know when I was auditing my payouts, I found several transactions that no longer existed because of being on the wrong branch of a soft fork.  However, for each forked transaction I found, I also found a replacement transaction from the pool making sure I got my earned coin.  Had a different transaction ID though.  I'd look and see if that tx is still in your payout history, and if not, if there's a different transaction of the same value paying you out.