Umm. I usually skip right over using the htpasswd program from apache and just write the file directly from Perl.

my $PASSFILE="/pathto/file/.htpasswd";
open(WRT,">$PASSFILE");

my $id_password;

# this is where I pull the list of id's
# and passwords from a database or file,
# then populate $id_password->{id}=pass;

$id_password->{'richard'} = "mypass";

foreach my $id (keys %{$id_password}){
  my $pass  = $id_password->{$id};
  my $pass2 = crypt($pass, "Ce");
  print WRT "$id:$pass2\n";
}

close(WRT);
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You can use other two letter combinations in the seed part of that crypt statement. "Ce" or "xV" or whatever.