Fist off, that doesn't compile.
Secondly, how did you solve it?
Thirdly, what if you have A.B.C=3&A.B=3, what happens then?
Your strategy is flawed, I can't fathom why you'd wanna do something like this.

Also, how could a user possibly cause "not a HASH ref" error? He's not writing any code.

#!/usr/bin/perl
use strict;
use CGI;

my $cgi = CGI->new( 'a.b.c=3&a.b.c=4&x.y=4' );
# convert somehow to:
my $args = {
    'a' => {
        b => {
            c => [3,4]
        }, 
    },
    'x' => {
        'y' => 4,
    },
};



use Data::Dumper;
warn Dumper $args;
die Dumper Shaz( $cgi );

#sub Shaz { "goes here -- you show me yours, i'll show you mine" }
sub Shaz {
    my( $cgi ) = @_;
    my $shazbah = {};
    for my $i ( $cgi->param() ) {
        my @bits = split /\./, $i;
        
        my $shazbot = $shazbah;
    
        for my $bit( 0..$#bits ) {
    
            if( $bit == $#bits ) {
                if( exists $shazbot->{$bits[$bit]} ) {
                    if( ref $shazbot->{$bits[$bit]} ne 'ARRAY'){
                        $shazbot = $shazbot->{$bits[$bit]} = [];
                    } else {
                        $shazbot = $shazbot->{$bits[$bit]};
                    }
                } else {
                    $shazbot = $shazbot->{$bits[$bit]} = [];
                }
                last;
            }
    
            if( exists $shazbot->{$bits[$bit]} ) {
                $shazbot = $shazbot->{$bits[$bit]};
            } else {
                $shazbot = $shazbot->{$bits[$bit]} = {};
            }
        }
    
        push @$shazbot, $cgi->param($i);
    }
    return $shazbah;
}

__END__
# I'd say this is pretty close

$VAR1 = {
          'x' => {
                   'y' => 4
                 },
          'a' => {
                   'b' => {
                            'c' => [
                                     3,
                                     4
                                   ]
                          }
                 }
        };
$VAR1 = {
          'x' => {
                   'y' => [
                            '4'
                          ]
                 },
          'a' => {
                   'b' => {
                            'c' => [
                                     '3',
                                     '4'
                                   ]
                          }
                 }
        };
[download]

update: Updated Shaz with actual code ;)(please note I did this in a single pass)

MJD says you can't just make shit up and expect the computer to know what you mean, retardo! I run a Win32 PPM repository for perl 5.6x+5.8x. I take requests. ** The Third rule of perl club is a statement of fact: pod is sexy.