Vista Command Prompt Problems?

Every time I try to run a batch file or an exe that runs as a batch file, command prompt will open up and disappear in a split. My situation: I am trying to use swantbls.exe to create lumps for my DooM map (yes, a doom map). When it runs, it is supposed to open up a Command prompt for manual file selection to use as a base for creating the lumps. I open it, it flickers, and I am unable to do anything with it. Are there any fixes?

My apologies if this is hard to understand, this is the best way I could explain it.

Update:

I'm already running it as administrator. The file extensions are correct. I don't know how to edit a .exe batch file. Thanks all for speedy responses.

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