reverting back to previous code, works fine once you use the correct mapping list

modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm

@@ -808,7 +808,7 @@ sub non_mapped_transcript_rescore {
       foreach my $target_tr (@target_transcripts) {
         my $mapped_target = $transcript_lookup{ $source_tr->id };
 
-        if ( $mapped_target ) {
+        if ( $mapped_target && $mapped_target == $target_tr->id ) {
           $found_mapped = 1;
           last TR;
         }
@@ -829,4 +829,5 @@ sub non_mapped_transcript_rescore {
 } ## end sub non_mapped_transcript_rescore
 
 
+
 1;