I don't know if it's improper usage or the plugin, but making the following change to class-frontend.php makes the filter I previously mentioned work properly for me. The commented line is the existing plugin code and the line below it the adjustment which makes it work properly for me.
foreach ( $whitelisted_extravars as $get ) {
//if ( isset( $_GET[trim( $get )] ) ) {
if ( get_query_var( trim( $get ) ) ) {
$properurl = '';
}
}