Someone can squeeze in and modify the log file between the time you've opened the file for append and the time you've thrown a lock on the file. The simple cure for this is to toss in a seek $fh, 0, 2; after the call to flock().

The next test seems to confirm that (Redhat Linux):

#!/usr/local/bin/perl -lw
my $file = "test.txt";
unlink $file;
if(fork) {
    open STDOUT, ">>$file" or die "Can't write to file: $!";
    $| = 1;
    print "first";
    sleep 3;
    print "third";
} else {
    open STDOUT, ">>$file" or die "Can't write to file: $!";
    $| = 1;
    sleep 1;
    print "second";
}
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first
second
third