I think the problem lies with Tie::Autotie. If you leave it out, things Just Work:

#!perl -w
use strict;
use Tie::IxHash;

tie my(%hash1), 'Tie::IxHash';

$hash1{ test }= 1;

tie my(%hash2), 'Tie::IxHash';

$hash2{ foo }= 1;
$hash2{ bar }= \%hash1;

print "H2: $_ => $hash2{ $_ }"
    for keys %hash2;


print "H1: $_ => $hash1{ $_ }"
    for keys %hash1;


__END__
>perl -wl tmp.pl
H2: foo => 1
H2: bar => HASH(0x378998)
H1: test => 1
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Looking at Tie::Autotie, it mentions your situation as a bug. "Assigning a reference" does not work. That's what you do with $hash2{ "b" }= \%hash1.