I think there are some Dictionary issues where recommended taxon names do not have entries in Index_Taxon_Name, but I have also come across situations where over time Dictionaries have  not updated properly. I have done an XML Report   available at http://forums.nbn.org.uk/uploads.php?file=JNCC_sy07Y_DictionaryCheck.zip  which does some basic checks and will indicate if there are Dictionary problems (it works on Dictionaries Upgraded to Y ).  This is run from Reports/System Reports/Information/SY07Y Dictionary Stats Check (Y).  It shows tables where the number of system supplied records are not in line with a Dictionary updated  to update Y. 

It may show some small differences which are not important, but any major differences would suggest a problem which needs correcting.

A Beta test version of the latest Dictionary Synchoniser is available if needed.

I  think this shows that you  don't have an issue with the dictionary updates. The problem must be in the actual Dictionary.  It will need a bit more research to find out exactly what is wrong.