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I think .zip files do not have file access bits, so Stuffit has to use full access. One of the access features in Unix (and thus OS X) is execution access, so all files coming from .zip will have execution bit on. Since OS X does not recognize the file, all it can tell is that it has execution bit on. Normally only executables (i.e. programs) has them, so all files look like programs.
You have to ask what to do with the .zip from the site you downloaded the .zip, or open Terminal.App, go to the folder where you unzipped the file and type "file thefilename". The file program uses a database that knows quite a lot of file types, it might give some hint.
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