To resolve this issue there are few checks that can be done:
Please check that there are no search criteria in the enquiry screen that might exclude nominal codes from the results.
Try running the enquiry search for various periods to see if the problem is limited to a single period, or affects all periods.
If these checks have not resolved this issue, Support will need to investigate further and probably run some scripts on the database. Therefore please raise a new case online and reference the title of this article and please provide as much information as possible about the totals that are not balancing.