You have a race condition [but see update below] by closing and dropping the lock between reading and writing the file. Do both within the same lock with the '+<' mode of open.

$completeadd = "counter.txt";
open MFILE, '+<', $completeadd or die $!;
flock(MFILE, LOCK_EX) || die $!;
chomp($filedata=<MFILE>);
$filedata++;
seek MFILE, 0, 0;
print MFILE $filedata, $/ or die $!;
close MFILE or die $!;
[download]

You seem to be trying to set up the sacrifice file as a semaphore, but once in place you don't use it for anything.

Update: Oops, now I see the semaphore ought to be effective. Your symptoms indicate that it isn't, however. Is the counter opened elsewhere by something that doesn't honor the semaphore?? Thanks, ++davido.