I'm running QXP 10.52 on OSX 10.10.5. We process a job containing multiple adverts that come from various clients and some contain RGB elements and/or transparency. I want to insert the advert PDFs into Quark and create a PDF/X-1a file colour managed to our CMYK profile. This is what we normally do and it works well, albeit we don't usually have RGB PDFs on the document.
What happens in most cases is what I would expect - providing "Color Manage Vector EPS/PDF" and "Include Existing Vector EPS/PDF in Layout" are ticked on in the Color Manager in Preferences the PDF/X-1a file is created and is obviously all CMYK. If those two options are not ticked on I get an error saying "The PDF was created successfully, but it failed the PDF/X1a evaluation", which is correct as the RGB PDF is not being colour managed to CMYK and so can't be a PDF/X-1a file.
However at least one advert PDF gives the same warning even when the two colour management options are turned on. The resulting PDF is still RGB. This is a problem. The advert is a PDF 1.5 file with transparency. I get the same result even if I use a flattened PDF 1.3 version of it in Quark. The log file says "Error- Uses color other than 4c or spot (14 matches on 1 page)"
Does anyone know why is Quark not able to convert the PDF to CMYK? It's driving me mad

Thanks,
Iain