Running the following SQL  produces a fairly long list, some of which looks OK. I thought that the indicator was supposed to be correctly set, but NHM would need to confirm this. 

SELECT INDEX_TAXON_NAME.ACTUAL_NAME, INDEX_TAXON_NAME.COMMON_NAME
FROM TAXON_VERSION INNER JOIN TAXON_LIST_ITEM ON TAXON_VERSION.TAXON_VERSION_KEY = TAXON_LIST_ITEM.TAXON_VERSION_KEY INNER JOIN INDEX_TAXON_NAME ON TAXON_LIST_ITEM.TAXON_LIST_ITEM_KEY =INDEX_TAXON_NAME.TAXON_LIST_ITEM_KEY WHERE TAXON_VERSION.UK_NATIVE=0

The Report Wizard generates the following query where UK native is set to 'No' (false) which on the surface of it also looks ok

SELECT Distinct Taxon_Occurrence.Taxon_Occurrence_Key AS Occurrence_Key, 'T' AS Type, Convert(char(16), null) collate SQL_Latin1_General_CP1_CI_AS as SURVEY_KEY, Convert(char(16), null) collate SQL_Latin1_General_CP1_CI_AS as SURVEY_EVENT_KEY, Convert(char(16), null) collate SQL_Latin1_General_CP1_CI_AS as SAMPLE_KEY, Convert(char(16), null) collate SQL_Latin1_General_CP1_CI_AS as LIST_ITEM_KEY , Convert(char(1),Null) as [Sample Type] into "#REPORT_OUTPUT" From ((((((Taxon_Occurrence LEFT JOIN Sample ON Taxon_Occurrence.sample_Key = Sample.Sample_Key ) LEFT JOIN Taxon_Determination ON Taxon_Determination.Taxon_Occurrence_Key = Taxon_Occurrence.Taxon_Occurrence_Key and Taxon_Determination.Preferred = 1 ) LEFT JOIN Survey_Event ON Survey_Event.Survey_Event_Key = Sample.Survey_Event_Key ) LEFT JOIN Index_Taxon_Name ITN ON (ITN.Taxon_List_Item_Key = Taxon_Determination.Taxon_List_Item_Key and ITN.System_Supplied_Data=1) ) LEFT JOIN Survey ON Survey.Survey_Key = Survey_Event.Survey_Key ) LEFT JOIN Taxon_List_Item ON Taxon_List_Item.Taxon_List_Item_Key = ITN.Taxon_List_Item_Key ) LEFT JOIN Taxon_Version ON Taxon_Version.Taxon_Version_Key = Taxon_List_Item.Taxon_Version_Key WHERE Survey.Survey_Key NOT IN (SELECT Survey_Key FROM User_Survey_Restriction USR WHERE USR.Name_Key = 'LC00000100000001') AND ((TAXON_VERSION.UK_NATIVE = 0))
WHERE (((TAXON_VERSION.UK_NATIVE)=0));

Sorry a bit of my SQl was missed in the paste. However on reflection there is definitely something wrong here as the majority of the taxa have a 0, which implies that they are not native which is onbiously wrong. Perhaps it is a simple as the indicator just being the wrong way round, but perhaps there is a bigger issue here than this. I have asked JNCC if they know what the situation is.