$box{$X}{$Y}{$z} =  1;             # DOES work 
#      $box{$X}{$Y}{$z}{'rect'} = 1 ;     # 'works' because it's comme
+nted out
#      $box{$X}{$Y}{$z}{'rect'} = undef ; # see above
       $box{$X}{$Y}{$z}{'text'} = 2;      # refs error
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The reason the last line gives an error is that it does the equivalent of

my $z = 1;
$z->{'text'} = 2;
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The 2 lines above it don't work if you take away the # at the begining of the lines.

A hash of hashes can be automatically created, but perl will not convert a scalar value in it to a hash unless it's undefined. By setting $box{$X}{$Y}{$z} = 1, you prevent $box{$X}{$Y}{$z} from being a hash.

Personally I always find that if you write this as

$box{$X}->{$Y}->{$z} = 1;
$box{$X}->{$Y}->{$z}->{'text'} = 2;
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it's much more clear what's going on, though it's more typing.

Update:
Try doing this instead:

$box{$X}{$Y}{$z} =  undef;
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if you really want to create the 'depth' of that HoH.

Update2:
Though you really don't need it:

       $box{$X}{$Y}{$z}{'text'} = 2;
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on it's own (without the preceding 3 lines) works perfectly.

See also perlref