PPLNS pools, and other non-true-PPS pools, simply have variable random luck determining your payout.
The fees have to be taken into account with PPS
Both fees and pool management have to be taken into consideration with PPLNS
Ignoring all fees, PPLNS is sometimes above the PPS value and sometimes below the PPS value.
Of course there is also the issue of how pools perform for PPLNS pools
Many pools like to blame luck on all their poor results, but a varying % of those luck results are caused by poorly maintained pools (like what happened with slush a few weeks ago getting many orphans)
Other pools, like Eligius, have always been getting more orphans for many years, and thus you lose out because of that also.
In general also, the % of lost blocks (which most pools probably wont show all of them) is dependent on how well managed the pool is and how well it is connected to the rest of the bitcoin network.