The reports in question had been created in FRx which was rather more forgiving that Management Reporter is for these things. The client had quite a large number of reports which may, or may not, have had segments entered in lower case so the client didn;t want to have to check and update manually.
I again delved into the Management Reporter SQL database and updated the ControlRowCriteria table to capitalise the Low and High values of the link to financial dimensions using the script below:
UPDATE ControlRowCriteria SET High = UPPER(High) WHERE LEN(High) > 0 GO
Once the update had been run, the client checked their reports and confirmed that they were now returning the correct figures.