Why are my identically coloured opaque images printing different colours? Is it a transparency issue

I have an object that is a plain white logo with a grey background - the file is a flattened psd file and has only the one layer.
when i place the logo into InDesign (CS5) onto a plain grey (the same colour as in the logo) background and print this simple combination, the grey background on the logo is a funny colour compared to that on the document background. they have the exact same RGB reference! they only appear different colours when printed; on screen they look great.
i thought that this was an issue with transparency and have tried playing around with having a transparent logo with no background and various transparancy flattener settings but nothings fixing the problem. the only thing that i managed to achieve was to make all of the grey one colour, but the funny coloured grey i was seeing just in the logo background!
when i go to window-output and check the flattener preview, i can see that i have no transparent objects whatsoever in my document.
any help on this matter would be greatly appreciated - its driving me MAD!
thanks,
becky

More to the point on this, I think, is that both RGB and CMYK values listed for any spot color are "best approximations" (many, perhaps most, spot colors have no good CMYK equivalent, and that would be true as well for some subset using RGB) using Pantone's unknown color space. Even in that space the probability of getting an actual match between the simulation and the true spot ink is close to zero. Using some other space makes things worse, and since there is no way to know the sapce in use at Pantone, you're kind of up the creek.
For CMYK converison you can do reasonably well by using the Ink manager to convert the spot to process and check the bok to Use Lab Values at the same time. For RGB, I have no idea how to come close, at all.

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