I apologize in advance if I am stating things you already know/considered.

The Deepbit stats page is delayed by one hour so you may be seeing blocks that were found prior to your starting mining.  Also if there is a really long block mixed in the round it may take longer than an hour for the stats page to be updated.

Also Deepbit doesn't find every block.  So a round may encompass several blocks worth of hashing and those shares are paid by the one block that got solved at the end.

Also when I first started mining I was switching my miner between Proportional and PPS whenever the luck shifted and the share count shows both share types for the block/round but only calculates pay based on the Proportional shares so it made it look like I was getting paid less when in reality I wasn't.

So it would seem to me that you need capture the share count for the round which may be more than one block long and match up the actual times so as not to be confused by the delay, if that's the case.

Anyway just some random thoughts, don't know if it has any bearing on your issue,
Sam