To retain transparency and color space you should export as PDF/X-4, a PDF without flattening.
I suppose the PDF export was similiar to PDF/X-3 as X-3 allows RGB and CMYK in the same file. If an object with transparency is above another object the color space of the upper objects wins. Non affected objects are do not change the color space.
With grey scale image I strongly recommend to use GREY images or CMYK with K only used.
If you would have exported to PDF/X-1a everything would have change to CMYK.
There is also a problem, objects with vectors are handled different when it comes to flattening than pixel objects. If you have a logo, I think you should a vector file, best AI or PDF/X-4.
If you have only RGB images with transparency you could change the blend space from Document CMYK to Document RGB.
the page containing the transparent logo the image is converted to CMYK
How are you determining that the image has been converted to CMYK? Have you checked its space with AcrobatPro's Object Inspector? I'm not seeing a conversion when I export to either PDF/X-4 or High Quality Print—both keep transparency live and object color unchanged. Here I've exported a page with transparency to PDF/X-4, with the blend space as CMYK. You can see the image remains as AdobeRGB.
The ID document's blend space is sent with the PDF, so as Peter suggests, you might want to try RGB. It may be that your RIP is handling the color conversion differently because of the blend space.