Hi Matt
Rather than answer your question directly, if I can explain a bit of background I hope it will save you and others a lot of time. In theory, the Report Wizard is able to detect all the synonymous names for something when you report on it. For example, if you select Chiroptera from the Mammalia list with the Expand Taxon Groups checkbox checked, then anything within the branch of the list starting at Chiroptera will appear in your report, even if it is a synonym or a term from another list. The problem stems from the fact that the dictionary supports 2 methods of identifying when 2 terms from 2 different lists actually represent the same taxon. We have been discussing with JNCC changes for the next release that will standardise on one of these methods.
To test if this was your problem, I went to Rhinolophus ferrumequinum in the Taxon Dictionary and compared the entry in the Mammalia list with the Recorder 3.3 list. What I noticed was that the "Other checklists" section on the right for each entry did not include the entry from the other list. This indicates that the dictionary does not contain the correct links to identify these 2 terms as the same thing using the original method. Fortunately the new method (driven by the NAMESERVER table) does identify these as the same thing because they have the same recommended taxon list item key.
The good news is you can change an option in Recorder to change which of the 2 methods it will prioritise when trying to calculate the list of terms that mean the same as the item you have selected. Go to the Tools\Options dialog and check the box titled Use Full Translation of Preferred Term on the General tab. This will enable the NAMESERVER powered method which as you have observed, is generally a lot more accurate. Hopefully if you do this, you can then use the Report Wizard to report on Chiroptera from the Mammalia list and it will pick up any bats from any list including Recorder 3.3.
As to your original Rucksack question, if you use the recommended taxon list item key in the rucksack and report on it, then you will have the same issues as before unless you check the Full translation option, because the old method of identifying terms that mean the same probably won't recognise the Recorder 3.3 bats as being the same as the Mammalia bats.
Best Wishes
John van Breda
Biodiverse IT