Made two changes recently that appear to have dramatically improved things again.
1) A further undocumented config tweak by Meru support
2) Turning off band steering - basically we don't have quite enough coverage on the 5Ghz band. Previously clients would move to a band and then the controller would roam them in an attempt to get the best throughput - which changes as people move about the school.
Also I suspect that the MS DHCP via relay issue recently fixed by MS (but worked around by Meru in our case) may also yeild and improvement for people.