Percolator in Proteome Discoverer 1.3

A new feature in Proteome Discoverer 1.3 is the Percolator program that was previously bundled with the Sieve program.  I have been running a few data sets with both the Percolator and with Thermo's Peptide Validator to determine which would be the best for our datasets.  One run of 48, reasonably complex samples, that I performed over the weekend ran like this:
1) Started processing around 4:30PM (sending results to the Mascot at our local cluster)
2) Mascot results received a little after 9:30PM (5 hours)
3) Percolator ran for 8-12 HOURS!  I am uncertain about the time since PD claims that Percolator ran 8 hours 41 minutes, but it started around 9:30 PM, but the clock says it finished around 9:00 AM.  Weird 4 hour time differential I can't possibly justify today.
4) Itraq reporter ions quantified and assigned to ions in roughly 20 minutes.

This is performed on a Power PC with a Xeon Quad-Core with >50 GB of RAM and striped hard drives.  Optimized for pure computational speed.  I'm currently re-running this same data set using the Peptide Validator.  If the data is not significantly better with Percolator, there is no way I can justify this additional time for processing.

Researching Percolator has identified this paper as the original reference.  I'll post more after I work through it (probably lunch time reading today).