Like sgifford, I believe the problem lies in writedata or release_lock (or in some other code you've not shown us).

I also believe your code should be cleaned up a bit, such as:

#!/usr/bin/perl
use warnings;
use strict;

use Fcntl qw':flock :seek';

our $COUNT_FILE = 'mycounter';

my $cfh;
-e $COUNT_FILE
  ? open $cfh, "+< $COUNT_FILE"
  : open $cfh, "+> $COUNT_FILE"  # not needed if file always exists
    or die "Can't open $COUNT_FILE: $!\n";

flock($cfh, LOCK_EX) or die "Can't lock: $!\n";

chomp(my $count = <$cfh> || '');

seek($cfh, 0, SEEK_SET);
print $cfh ++$count, "\n";

print "Run #$count\n";

# truncate not needed as $count is always increasing
close($cfh); # automagically releases the lock
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bbfu
Black flowers blossom
Fearless on my breath