Hi Ian,
In order to get a under-the-hood look at this, I’ll need you to enable some debugging options.
First of all, can you provide the template code for the template that is causing the trouble?
Now, in the Control Panel, navigate to Admin->System Administration->Output and Debugging. Set “Display Output Profiler?” and “Display Template Debugging?” to “Yes” and click Submit. This output will only be shown to logged in Super Admins.
Once you have that on, visit the template in question and look for the area regarding SQL queries. It will tell you how many queries have run to generate the page and give you the option to see the queries that were run.
You can post that here too, so we might see if anything stands out.
Cheers,