It can be very complicated to work out what is going on with issues like this and I will work through the detail as soon as I can, but I think the following is most probably the reaon why there are problems.

There seems to be three  different issues here. In order to get the Common names R6 first uses common name attached to the list, then if there isn't one the name attached to the preferred name, and finally the name attached to any list. If this isn't done then many taxa would not have common names, because not al lists (even the preferred ones) have common names.  Unfortunately, this means that it is sometimes picking up names which come from badly formed entries in some lists. There is a mechanism for making adjustments in these cases and when I  have  investigated this one in detail and make the necessary change.

The other issue is with the report Wizard. At the moment this uses Index Taxon name to work out which taxa should  be included in reporting. If any list has  a link (right or wrong) then this will be taken into account,  so badly formed entries in any list  will affect the results. Now we have the Organism table we can avoid using the badly formed list to obtain the related  taxa and this is one of the proposed changes for release 6.20. Alternatively once we know what is happening Chris may be able to make a change which overcomes the problem.

The query which poulates Index_ taxon_designation also uses the relationships in Index_taxon_name and also suffers from the same problem in that it will use information from badly formed entries to expand the  the taxonomic hierarchy.  Again it should  be possible to resolve this now we have the Organism table.