Well, the code you show can't possibly work, because you have keys($foo) in a couple of places when it should be keys(%$foo)

Probably your best bet would be to reduce your code to a simple test case that still shows the problem, then post the whole code here if it still fails. The very process of reducing the code often turns up where the problem is.

And my a simple case, I mean simple; ie remove all the XML and file reading stuff, and replace the heart of make_var_hash with something like

if ($xml eq 'file1') {
    $myhash{foo1} = ['bar1', 55 ];
    $myhash{foo2} = ['bar2', 55 ];
}
elsif ($xml eq '...
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