thanks, yes i did have use strict and warnings enabled, Im not sure its a scoping issue as the $twig is a global and it does run without giving errors, just not the results I expected!
if I put all the sub code into the foreach loop I still get the same problem, namely that the last file is the only one which is apparently parsed: I missed some bits of code out before as I didnt think they were relevant and was trying to avoid inflating the post with unimportant details.. heres the fuller version:

#! /usr/bin/perl -wT


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

### UNTAINT ENVIRONMENT, SUPPLIED FILENAMES

#code to untaint env, filames here


my $twig;
my ($xmlfile, $ctlfile, $config);
my (@assm_header, @chain_header, @xmlfiles);
my %assm_header = ();
my %assm_line   = ();
my %pdb_line = ();
my %chains = ();
my %chain_header = ();

### HANDLE COMMAND LINE OPTIONS

# code to handle Getopt::long here

@xmlfiles = qw(file1.xml file2.xml);


foreach my $xfile (@xmlfiles)
{  

 $twig = new XML::Twig(
                         twig_roots =>  {
                        'pdb_entry/pdb_code' => \&pdb_entry,
                        'pdb_entry/total_asm' => \&pdb_entry,
                        'pdb_entry/asm_set/assembly' => \&assembly,});


   # &parse_twig($xfile); # sub code now inserted below

   ## sub code folded into here

   if ($twig->safe_parsefile($xfile) == 0)
   {
      die "Failed to parse $xfile: $@";
   }

   my $root = $twig->root;
   my @params = $root->children('pdb_entry');
   $twig->purge;
   $twig->dispose;

 }



...
 
handler code
[download]

result is file2 gets parsed and output, no sign of file1.. ;+(