I'm moving your question to the InDesign forum.
Can anyone advise how we correct this as we are supplying PDF files to print, and getting the incorrect colour back, which is causing huge corporate identity problems.
If your document is all CMYK color export the PDF with no profile. In that case the color will export as DeviceCMYK and the values will output unchanged unless someone downstream forces a conversion. PDF/X-1a exports flattened CMYK with no profile. PDF/X-4 also exports native InDesign CMYK colors as DeviceCMYK.
How was the original PDF created and saved?
Does it just contain the logo?
In which colour mode are you opening it in Illustrator, CMYK or RGB?
Are the colours process or spot?
How are you copying it into InDesign? It's generally better to save as AI or PDF, and place.