I'm guessing it's related to the incorrect use of the "g" modifier in scalar context. Even if it isn't, the following is still buggy:

  next if(/^#/g);
  next if(/^\n/g);
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Also, you check for empty lines, but not for lines that contains nothing but spaces.

How about:

while(<IFH>) {
  s/#.*//;
  if (s/\\\s*$//) {
    $_ .= <IFH>;
    redo;
  }
  s/^\s+//;
  s/\s+$//;
  next if !length();
  $line .= $_;
}
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