I have managed to get a workround by calling the parser from another program which feeds it one file at a time:

#! /usr/bin/perl 


use strict;
use warnings;
use Fcntl;
use Getopt::Long;
use POSIX;


my ($xmlfile, $ctlfile, $config);
my @xmlfiles;

### HANDLE COMMAND LINE OPTIONS

GetOptions('config|c=s'     => \$config,
           'ctlfile|ctl=s'  => \$ctlfile,
           'xmlfile|x=s'    => \$xmlfile,);


if ($xmlfile) # xmlfile specified on cmd line
{
   ($xmlfile = $1) = $xmlfile =~ /^(\w+\.*\w+)$/i;
    push @xmlfiles, $xmlfile;
}
elsif ($config) # xmlfiles in config file
{
   sysopen(XMLFILES, $config, O_RDONLY)
     or die "Can't open $config : $!";

   my @config = <XMLFILES>;
   foreach my $line (@config)
   {
      next if (($line =~ /^#+/) || ($line =~ /^\s+$/)) ;
      chomp($line);
      push @xmlfiles, $line;
   }
   close XMLFILES;
}
else  # try default filename then bale out
{
   $xmlfile = "multimers.pisa",  if (-e "multimers.pisa" and -s "multi
+mers.pisa");
   if ($xmlfile)
   {
      print "Using default xml file $xmlfile\n";
     ($xmlfile = $1) = $xmlfile =~ /^(\w+\.*\w+)$/i;
      push @xmlfiles, $xmlfile;
   }
   else
   {
      die "No valid xmlfile specified...exiting\n";
   }
}

foreach my $file (@xmlfiles)
{
   system "xml_pisa.pl $file"; # this calls the original              
+         
                               #  twig parsing script 
}
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