I found today that the following seems to work - not sure why yet:
Clone a report, edit the template, save it in Word and close, then save in SIMS. Open the template again, click somewhere random on the template (not making any changes) then close Word and save in SIMS. Running the report should then work.
I've found that running the report straight after editting the template doesn't work, the fields don't pull through, however opening the template once and then running it does work.
Any changes to templates (which were created in Office 2003 at least) seem to require this process.
Investigations continue...