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I ran the tool on a accc file I had lying around and here's the profile dump:

accc_report.profile% sort cumtime
accc_report.profile% stats 5
Mon Aug 05 14:07:37 2013    accc_report.profile

         44061406 function calls (44061393 primitive calls) in 160.941 seconds

   Ordered by: cumulative time
   List reduced from 2713 to 5 due to restriction <5>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1   64.068   64.068  161.037  161.037 accc_report.py:15(<module>)
  5786418   47.012    0.000   47.012    0.000 {method 'index' of 'tuple' objects}
     4802    2.327    0.000   25.199    0.005 .\pssarrays.py:1239(accc_solution)
     1200    0.646    0.001   11.804    0.010 accc_report.py:544(GetN1results)
        1    0.048    0.048   10.357   10.357 accc_report.py:517(BuildMasterConlist)

Things i noticed:

• Most of the time is spent on the 5786418 calls {method 'index' of 'tuple' objects} at 47sec.
• Actually gettting the data using pssarrays.accc_solution() is quicker than I remembered at 25sec.
• excelpy is only 7sec which may be completely inaccurate, excel via COM threw some warnings when writing the xls file. I just grabbed a random accc file so the comparisons were probably meaningless.

I'm not sure what is hammering the {method 'index' of 'tuple' objects}. A small refactor to break up some of the main loop into functions would give us some hints, or you could figure it out just by staring at the code for a while.