Probably not; however, there are known issues with MMCFE, which is the most widely used front-end for pools. I have noticed that with several Alt coins(especially those with a low difficulty) MMCFE does not reward the users for some blocks.
Run this on your database to see if this is happening to you...
SELECT blockNumber AS unpaid_blocks FROM `winning_shares` WHERE blockNumber NOT IN (SELECT assocBlock FROM ledger)
The result here will check winning_shares against your ledger, and tell you which block numbers do not correlate.
Until I have a repair, and automatic payment method for these unpaid blocks I will be offering this list to the users of
http://dgc.turbocoin.us and our other pools upon repair.
Maybe other operators can report back here from their various coins to see if particular coins have an issue or low difficulty, or low confirm requirements causes it.
Thanks.