Executable behaving different when called f/Java

I have an executable that is run from the command line which behaves differently when I run it from my application. The executable takes MP3s files as arguments and merges them together. When I use large files from within my app, it doesn't respond, but using the same files from the command line works fine. I was thinking it might be a memory thing, but the executable should get its own space seperate from the VM. Does anyone have any suggestions? Thanks!

I do not have the source for the executable, so I wouldn't be able to pull lines out of there. It works from my Java app when I pass in smaller files, so I know I have the syntax correct, but with larger files it hangs. When I run the same thing from the command line with the larger files it runs like a champ. I was trying to use my task manager (I'm on Win NT) to look at memory usage since the only variable seems to be file size, but nothing seems to indicate it is a memory issue.

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