I do exactly the same thing you do, but instead of running the process every now and then, put a signal handler in front of it, and ...

.
.
.
while(1)
{
  while(my $line=<$fh>)
  {
    # lot's o processing
  }
  sleep 5;
}
[download]

When I don't need or want to process anymore, just kill the process via the prepped signal handler, so i can clean up db handles or whatever i'm doing, gracefully.

Doesn't solve your exact problem, but gives you a new possibility. -s