You need a bindParam() call for each ? in the SQL statement... so you probably need:
<?php
$rsBySubject = new WA_MySQLi_RS("rsBySubject",$connProjMain1,0);
$rsBySubject->setQuery("SELECT books.isbn13, books.coverimage, books.title, books.full_title, books.subtitle, books.subject1, books.subject2, books.auth_id, books.publisher, books.`description`, authors.authfirst, authors.authlast, authors.auth_id, authors.author_full FROM books, authors WHERE books.active_web = '1' AND (books.subject1 LIKE ? OR books.subject2 LIKE ?) AND authors.auth_id = books.auth_id ORDER BY authors.authlast");
$rsBySubject->bindParam("c", "".(isset($_GET['subject1'])?$_GET['subject1']:"") ."", "-1"); //colname
$rsBySubject->bindParam("c", "".(isset($_GET['subject1'])?$_GET['subject1']:"") ."", "-1"); //col2name
$rsBySubject->execute();
?>