I never convert to PDF myself, but you could try one of the following settings on the Convert - Look&Feel page when you convert:
- If it isn't already, try CHECKing the first item - 'Disable font size rescaling'.
- Alternatively, if you prefer to have that box UNCHECKED have a look at the values in the 3rd item on the same page - 'Font size key'. You need to make sure the last value is big enough to accommodate the font-size setting for your headings in the source epub.