Please "use strict;" and "use warnings;", particularly if you are a newb.

Did you increment $readcounter ? Working code:

use strict;
use warnings;
my @data;
my $readcounter=0;

while (<DATA>) {
      chomp $_;
      my @line_array = split(/[()\t+\s+]/, $_);
      my @full = map {$_ ? $_ : ()} @line_array;
      @{$data[$readcounter++]} = @full;
     # My preference## $data[$readcounter++] = \@full; # No Copying 
     # -- Better (but more complex next line:)
     ## $data[$readcounter++] = [ map {$_ ? $_ : ()} split(/[()\t+\s+]
+/, $_)];
}
@data = sort { $a->[0] <=> $b->[0] } @data;
print qq|@{$_}\n| for @data;
__DATA__
00000(IDR) 86480 22 41.435 40.696 40.728167 0 FRM 3
00002( P ) 35248 24 38.568 39.327 40.641 253 53 FRM 2 
00001( P ) 35238 24 38.568 39.327 40.641 253 53 FRM 2
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Update: Most perl programmers would avoid the use of a "$readcounter", and write it as:

  push @data, \@full; # Auto-increments, and appends to @data
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