There is an awful lot of ... misunderstanding going on in this thread, and it is mostly caused by you wrongly describing the problem. Until you post the scripts that I can run that demonstrate the problem you are describing, I do not believe what you are saying is happening is possible.

For example, save the following three scripts and run them, and barring some external influence, like disk full, disk failure, or a third party piece of software taking exclusive access to the interchange file, it will run forever without errors.

##609823.pl
#! perl -slw
use strict;

my $count;
while( 1 ) {
    print "Iteration: ", ++$count;
    system 'perl 609823-1.pl';
    system 'perl 609823-2.pl';
}



## 609823-1.pl
#! perl -slw
use strict;

my $count = int rand 100;
open OUT, '>', 'output.txt' or die $!;
print OUT 'A line of junk' for 1 .. $count;
close OUT;

printf "Wrote $count lines \t";


## 609823-2.pl
#! perl -slw
use strict;

open IN, '<', 'output.txt' or die $!;
my @lines = <IN>;
printf "Read %d lines \t", scalar @lines;
close IN;
unlink 'output.txt';

## Produces
c:\test>609823
Iteration: 1
Wrote 72 lines  Read 72 lines   Iteration: 2
Wrote 19 lines  Read 19 lines   Iteration: 3
Wrote 97 lines  Read 97 lines   Iteration: 4
Wrote 58 lines  Read 58 lines   Iteration: 5
Wrote 94 lines  Read 94 lines   Iteration: 6
...
[download]

All of which is just a long winded way of saying: There is something that you are not telling us going on here, and the quickest way of clarifying what that might be, is for you to show use the contents of the script you are using, rather than hypothetical equvalents which obviously aren't.