I've exported a pdf document but the png images suddenly have a different coloured background (as opposed to a transparent one).
The png is over a dark footer, but when exported to pdf a box appears around the png image.
Is there an export setting I'm missing or do I need to import the png files differently?
If export to PDF is the ultimate intent, PNG may not be the best choice of image format. Aside from that, you'll want to investigate and consider how transparency in your document may be interacting with color.
Have you used spot colors? CMYK? RGB?
What is the Transparency Blend Space setting?
Is the PDF destined for print? On-screen? Both?
With answers to these questions, it will be much easier to offer advice that will align with your broader objectives.
Where do the PNG come from?
PNG are only in RGB without color management, better would be to use AI, PDF/X-4 or if only pixels are inside a PSD file.