It appears that pages that were already missing a vw_counter record before upgrading to version 4.0.4 did not get one after that upgrade. Whatever bug this is was resolved already (because new pages get vw_counter records as expected), but I have added a step to the upgrade for 4.0.9 to regenerate missing vw_counter records.
Unfortunately most views that occurred while the record was missing are lost forever (except whatever occurred in the last day or so). There is no way to know how many views there should have been during that time. Pages with a view-count of 0, such as views lost due to this bug, don't appear on Special:Popularpages.