mmm, at what point do you actually check if these files are there?
What I'd do, because it is a strange problem, is use perl -d to step through your code on the box where the problem appears, maybe set a breakpoint just before the archive is created and at that point check if the files are there and what their size is (or add print/system commands in your source code to debug, depending on your debugging style).
Another thing that might be going wrong when your script generates the files is that the file-content still is in the output buffer instead of on disk. You can set $|=1 to avoid this.
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