The following is your code, exactly copied and pasted from the JSfiddle you linked. Lines marked with // [*] show the problem.

if ((pass === pass2) && (pass.match(/^[a-zA-Z]+$/)) && (pass.length >= 6)){
    document.getElementById('pass').style.borderColor="green"; // [*]
    document.getElementById('pass2').style.borderColor="green"; // [*]
}


else if (pass !== pass2){
    document.getElementById('pass').style.borderColor="red"; // [*]
    document.getElementById('pass2').style.borderColor="red"; // [*]
    document.getElementById('messagepasslabel').innerHTML='password doesnt match confirm box.';
    return false;
}
else if (pass.length < 6){
    document.getElementById('messagepasslabel').innerHTML='pass needs at least 6 characters.';
    document.getElementById('pass').style.borderColor="red"; // [*]
    document.getElementById('pass2').style.borderColor="red"; // [*]
    return false;
}