GeoffR, I had the same problem with some non-DRM epubs. It's a little heavy handed but give this a try:
In the conversion options, under Look And Feel, select the "filter style information" tab. Check the "Fonts" box then in the "Other CSS Properties" add "font-size" (Other CSS Properties: font-size, line-height).
Checking the "Fonts" box will strip a lot of the font information from the epub (but not "font-size") and enable adjustment of fonts on the Kobo for some non-DRM epubs.
Calibre rev. 0.9.4
Kobo firmware rev. 2.1.5(r43939 10/12/12)