That's truly bizarre. Three recommendations. First, check the open and close statements, just to be sure: open (FILE2, ">$file") || die "can't open $file: $!"; Second, use select on your FILE2 filehandle to make that the default output. You can rewrite the problem area as:

select(FILE2);
$lineout = "$temp1 = $temp2\n";
print $lineout;
print STDERR $lineout;
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I removed the double-quotes because they're probably not necessary in this case. You might also use ">>$file" in the open statement for debugging purposes. It appends to the file.

The last recommendation is to print to STDERR the $temp1 and $temp2 variables after you split them. That's low on my list of things to check, though. Best of luck... that's all I can think of.