seems to be failing line count.

You're right. Because the regex can match a block of html and a block of asp in one go, in between $line already needs to be updated. So I removed the extra set of parens and the counter line again and added two new \n-counters: one for $1 and one for $2.

my @parsed;
my $line = 1;

while ($asp =~ /\G((?: [^<]+ | <(?!%) )*) (?: <%(.*?)%> | ((?=<%)) )?/
+gsx) {

    $1 and push @parsed, [ $line, html => $1 ];
    $line += $1 =~ tr/\n//;

    $2 and push @parsed, [ $line, asp  => $1 ];
    $line += $2 =~ tr/\n//;

    defined $3 and die "Unclosed ASP code block starting on line $line
+ near '",
        $asp =~ /\G(<%\s*\n?.*)/g, "'.\n";
}
[download]

/\G((?: [^<]+ | <(?!%) )*) (?: <%(.*?)%> | ((?=<%)) )?/gsx

Just for fun, I wanted to try to make a Perl 6 rule from this. Here it is, untested and mostly guessed. I have no idea how to do line numbers, so I cheated and imagined a method of .pos for that :)

rule code_begin ($type) {
    <{
        {
            asp => '<%',
            php => '<?',
            plp => '<:' 
        }.{$type} // fail "Unknown type: $type"
    }>
}

rule code_end ($type) {
    <{
        {
            asp => '%>',
            php => '?>',
            plp => ':>' 
        }.{$type} // fail "Unknown type: $type"
    }>
}

rule code_block ($type) {
    <code_begin $type> (.*?) <code_end $type>
}

rule code_document ($type) {
    [
        # First, match any number of subsequent code blocks.
        [
            { $?line := .pos.line }
            <code_block $type> ::
            { push @?blocks, [ $?line, code => $?code_block ] } 
        ]*
        
        # If there is now a code_begin, obviously that is an open bloc
+k.
        # (In PLP, that is valid, but let's assume for now that it's n
+ot.)
        [ 
            { $?line := .pos.line }
            <code_begin $type> \n* $?context := (\N<,15>) 
            { fail "Unclosed code block on line $?line, near '$?contex
+t'" }
        ]?

        # And then a piece of text.
        # (At least one character, to avoid having empty blocks.)
        [
            { $?line := .pos.line }
            $?html := (.+?) [ <before <code_begin $type>> | $ ] ::
            { push @?blocks, [ $?line, html => $?html ] } 
        ]?
    ]*    
}

my @parsed = ($asp ~~ /<code_document 'asp'>/).{blocks}
[download]

Juerd # { site => 'juerd.nl', plp_site => 'plp.juerd.nl', do_not_use => 'spamtrap' }