I have seen this problem before, due to multiple processes trying to read and write files simulataneously. Here is a more cautious style of locking using flock that hasn't let me down yet (probably adapted from the Cookbook, I can't remember):

# reading

open NEWSRC, "< $newsgroup_file"
   or die "Could not open newsgroup file $newsgroup_file\n";
unless (flock NEWSRC, LOCK_SH | LOCK_NB) {
   print "Contention: cannot get a shared lock the file, blocking ($!)
+...\n";
   unless (flock NEWSRC, LOCK_SH) {
      die "ERROR: cannot get a shared file lock on $newsgroup_file: $!
+\n";
   }
}
print "Initial newsrc read lock granted\n";
my @news_lines = <NEWSRC>;
close NEWSRC;

# writing

open NEWSRC, "+< $newsgroup_file"
   or die "Could not open newsgroup file $newsgroup_file\n";
unless (flock NEWSRC, LOCK_EX | LOCK_NB) {
   print "$group ($$): Contention: cannot get an exclusive lock the fi
+le,\n   blocking ($!) ...\n";
   unless (flock NEWSRC, LOCK_EX) {
      die "$group ($$): ERROR: cannot get an exclusive file lock on $n
+ewsgroup_file: ($!)\n";
   }
}
print "$group ($$): Write lock granted\n";
print NEWSRC @news_lines
  or die "Disk full\n";
close NEWSRC;
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-Mark