I've just found an earlier post that gives the answer. I had not linked my topics to a keyword.
Although, when I checked the properties, some already were linked to a keyword. But now, I have been through and linked any topics that werent linked to a keyword (that were supposed to be, I havent got that many at the moment) but still only a couple of the index entries are displaying in the output?
Yep, that would do it. 🙂
If you go to Reports > Index, does everything look OK there?
After opening the output, refresh the browser to make sure there isn't a cache problem.
My indexes are displaying correctly now so I think it must have been a caching issue, as you say. Thanks again for all your help.