Did you remove the email address form element? This is used by the contact form as the from address, an email with no from address will be treated as spam.
you could edit the WA_Universal_Email/WAUE_contact_1.php file, and change:
$MailFrom = "".((isset($_POST["Email_address"]))?$_POST["Email_address"]:"") ."";
$MailFrom = "firstname.lastname@example.org";
to hard code the from address.