I think I worked out why the above didn't work. See below image. With some of the reports, I added another data filter box alongside the report (example report 13 uses data filter 11). The results are corrected filtered using the overall Datafilter 1.
However for Reports 11 and 12, where I didn't add the data filter along side these, Datafilter1 was not being applied. So when I looked at the results from these reports, I had too many records.
Seems strange to me, but I think I can get it to work now.