Average results over batch of runs

I have an executable that I can run in AQTime.  However, I want to run this program around 100 times with different command arguments and then get the results totalled over all of the runs.  I have a ruby script to make all these calls as well as a batch script.  However, I can't figure out how to get AQTime to profile my executable in this situation.  I have tried attaching to the ruby process or to cmd.exe but AQTime does not profile the executable when it is called via a script.  I am making a system call to the executable in the same location that I have added it to AQTime's modules.  I assume this is a common thing to do, does anyone have a solution?

Thanks a lot,

Dan