Chomp just before the comparison:

my @sorted = sort{ 
my $one=substr($a,rindex($a,'|'));
my $two=substr($b,rindex($b,'|'));
chomp($one,$two);
($one <=> $two) } @database;
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Update: I only answered the question of where to put a chomp in that block. See the following replies for a more in-depth analysis of the sorting problem.

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Edit: chipmunk 2001-05-26