The bug was most likely the missing \ between the $dir and the $filenme. The following fixes that and is a little more Perlish than Cish:

use strict;
use warnings;

my ($dir1, $dir2, $testfile) = @ARGV;

opendir DIR1, $dir1 or die "Can't open directory $dir1: $!\n";
opendir DIR2, $dir2 or die "Can't open directory $dir2: $!\n";

my @onedir = readdir(DIR1);
my @twodir = readdir(DIR2);

closedir DIR1;
closedir DIR2;

for my $onefile (@onedir)
  {
  my $twofile = shift @twodir;
  next if $onefile =~ /^\./;

  $onefile = "$dir1\\$onefile";
  $twofile = "$dir2\\$twofile";
  Calc($onefile, $twofile, $testfile);
  }

 sub Calc
 {
 my ($onefile, $twofile, $testfile) = @_;
 print "$onefile, $twofile, $testfile\n";
 }
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