I think it's your ++$count that's the problem. The drive numbers are sequential, but you have lines that begin with 'robot'. You don't increment $count for these lines (good) but you do the system command (not so good). Perhaps you should skip out of the loop early if you run into a robot:

    next if /^robot/;
    $count++;
    system( ... );
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Without having anything named 'tpconfig' on my system, I can't check the man page for error messages, but I would be surprised if it allowed you to delete a drive you'd just deleted. The numbers seem to be fairly close.

Update: Here's a more complete code segment that really ought to do it for you:

my $drive;
my $count = 0;
open( LIST, "tpconfig -l|" ) or die $!;
while(<LIST>) {
    ($drive) = unpack '@0 A8',$_;
    next unless /^drive/;
    (system("tpconfig -delete -drive -index ${count}") == 0) or print 
+"Error deleting: $?";
    $count++;
}
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Starts at 0, doesn't execute the command unless it's found a drive. Increments the number after it executes the command, checks $? for errors. (I'm not 100% certain about the syntax of that system checking, but it was in perlfunc that way.)