At Jan's suggestion, I hacked the pedestal file that the database sees and manually set all the ped values to zero. I then ran over the M-C file to see what effect this would have.  The M-C file is found here: /star/institutions/iucf/balewski/star/institutions/mit/balewski/StarTrigSimuEvents/pythia_pT7-9_rcf1225.eve.bin-348k

The pedestal file I used is here.

The diagnostic files from the M-C data using the hacked pedestal file are here.

The diagnostic files from the M-C data using the pedestal file I've been using for all previous investigations (for comparison) are here.

The diagnostic files from the real data using the original pedestal file are here.

A quick comparison between the hacked M-C diagnostic plots and the real data diagnostic plots shows that setting all peds to zero makes the M-C data qualitatevly similar to the real data. For example, on page 5 for the hacked M-C, the eta-phi and phi1-phi2 plots show the same 'broken up' look as the real data as opposed to the more even filling of the original M-C plots. The hacked M-C also shows a large increase in the jet energy similar (though not in magnitude) to what we see in the real data. (The plots of jet energy don't appear in the hacked M-C because all energies are off scale and the log plots choke when there are zero values in the histogram.)

These observations lead me to think I need to investigate exactly which pedestal file I use for the real data.

Possible Solution

The behavior I saw above when changing the ped file led me to look closer at what pedestal file I was using. The pedestal file I had been using was from run 7160018 so I decided to try to use the most up to date file I could find in the setup directory. I used the file run9064005.l2ped.out in the directory:  /afs/rhic.bnl.gov/star/users/kocolosk/public/StarTrigSimuSetup/L2/2008/db/

I then ran over the 60k real events from run 9067013 and the diagnostic histos looked much closer to what one sees from the diagnostic histos taken durring the run. See http://online.star.bnl.gov/L2algo2008/jet/

It seems likely that the high ET jet problem was just due to my using the wrong pedestal file.