The problem is that you're splicing the main array, not the nested array, so everything after the found line gets pushed forward one, and the line gets found again endlessly. A better piece of code would be:

use strict;
use warnings;

my @R; # Constructing your matrix...
while (<DATA>) { chomp; push @R, [split(/ /)]; }

for (@R) {
    if ($_->[0] eq 'a') {
        unshift @$_, '#'; print join("\t", @$_)."\n";
    }
}

__DATA__
x y z
a b c
e f g
h i j
[download]

EDIT: And here's your code, modified so it works. I'd personally use unshift rather than splice, though...

for my $rc(@R) {
        if ($rc->[0] eq "a") {
                splice @$rc, 0, 0, '#';
                print "$rc->[0]\t","$rc->[1]\t","$rc->[2]\t","$rc->[3]
+\n";
        }
}
[download]

You were missing a > and a ; on line 4, btw.