I may have solved this one myself. It would appear that when we upgraded to 1.6, it was such a hard changeover (all 350 courses had to be backed up and restored individually), that in the changeover the course files were brought across in block. Consequently when courses were backed up and restored they had different ID numbers from the original and picked up files that were already in a section for that course. Hence the random nature of it.
I have deleted all course sections on the server with numbers above the latest 'mysql recognised course' and am keeping my fingers crossed.
Mike