If bikeNomad's solution doesn't work, just split the whole thing on tabs (untested): 
my $file;
{
  local $/ = undef; # learned something ;}
  $file = <>; #or <FILE>
}
$file =~ tr/\r//d;  #remove carriages

my @items = split /[\t\n]/, $file; #one array of items;
my $rowsize = 3;
my @AoA;
while( @items >= $rowsize ){
  push @AoA, [splice @items, 0, $rowsize]; 
}

[download]
.... this works only if you're garanteed to have 3 columns.

Hope this helps,

Jeroen
"We are not alone"(FZ)

In reply to Re: Parsing lines containing extra carriage returns by jeroenes
in thread Parsing lines containing extra carriage returns by ezekiel

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