I actually ran into a strange bug some time ago (under Apache 1.3.23) where if the salt I generated consisted of the same two characters (e.g. 'aa'), it wouldn't work under htpasswd. So here's the code I used:

    my @salt_chars = (a..z,A..Z,0-9,'.','/');
    my $salt1 = $salt_chars[int(rand @salt_chars)];
    my $salt2 = $salt_chars[int(rand @salt_chars)];

    while ($salt2 eq $salt1) {
        $salt2 = $salt_chars[int(rand @salt_chars)];
    }

    my $salt = $salt1 . $salt2;
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I'm not sure if this is still an issue; you might want to test it out on your system.