All the files in your script share one filehandle, FILE. You have two options to solve this problem: use Symbol::gensym() to create unique filehandles, or use lexicals instead of bareword filehandles. The latter option requires you to have a new perl (5.6 or 5.8, I can't remember). The code would look like this:

my $fh;
open($fh, "...") or die ...;
return $fh;
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