C++ program crash in batch processing only - c++

For a project, I've created a c++ program that perform a greedy algorithm on a certain set of data. I have about 100 data set (stored in individual files). I've tested each one of these files manually and my program gave me a result each time.
Now, I wanted to "batch process" these 100 data set, because I may have more to do in a near future. So I've created another c++ application that basically loops and call my other program using the system( cmd ); command.
Now, that program works fine, but my other program, which was previously tested, now crashes during that "batch processing". Even weirder, it doesn't crash each time, or even with the same data set.
I've been at it for the past ~6 hours and I can't find what could be wrong. One of my friend suggested to me that maybe my computer calls (with system()) the other program too quickly and so it doesn't have time to free the proper memory space, but I find that hard to believe.
Thank!
EDIT:
I'm running on Windows 7 Professional using Visual Studio 2012

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Process Explorer says:
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