I don't think this has anything to do with Perl.

All of your I/O comes through the shell. You are basically running a shell script to generate the file. There are some things I would look at for possible differences though:

1. Which shell is invoked by default? Is it the same shell?
2. Encoding differences. Is the same encoding happening? Do the files look the same in a hex editor?
3. iconv might show something interesting.

However what happens beyond within system call is OS dependent, not Perl dependent. There is really very little room for this to be solved as a Perl issue. What I would recommend doing is put the commands in a shell script and invoke that. If it works in the shell script but not from Perl, I would then start checking environment variables, etc.