All the tables are numbered correctly in document Sections 1-4 (Table 1-6) and Section 5 (Table 7), but the following Tables in Section 6 go back to Table #6 and on from there, as if Section 5 hadn't happened. I have tried deleting and re-inserting the caption for the table in Section 6 and I have tried selecting the whole document and hitting F9 to update fields, with no changes. Any suggestions?
Most likely the SEQ fields behind the table caption is being reset or skipped in some form or another. To have a look press ALT + F9 to show field codes and look for any SEQ fields belonging to "Table" which don't look like they are part of a proper caption. Additionally you can try looking for any SEQ fields which include the "\r" switch which can restart the numbering to a different value.