Custom PDF export changes colour from CMYK to RGB!

I've created a custom PDF output setting (based on the preset "Press") for hi resolution output. The files are created in inDesign CS5 - CMYK and several spot colours too. I can check the output-preview and it looks OK. When I check the output preview of the PDF (or the film/plate seps ahhh!) they have been converted to RGB. How do I keep the separations in CMYK?

Over the years I've learned plenty of lessons the hard way, and they're the ones that really stick.
In theory when sending an ad to various publications I'd try to send something that correct to each, but in practice that's essentially impossible, so I tend to convert everything to SWOP 2 (you'd be amazed how many newspapers use SWOP 2 COATED as the working profile in this country), admit that colors will never be perfect or match across multiple pubs because my clients can't afford the costs of making that happen, and leave out the profiles. I'd rather have crisp type than slightly better color from a conversion, but that's me.
But I do now include the profiles and I use the profile the printer tells me to use - the only way I'd get rich black type, I think, is if the printer ends up using a different profile than what they told me, right?
That's correct. If that happens, it's time to get another printer.
Including the profiles - I thought - would somehow let the prepress know "actually this file was made for a different print process".
I suppose it might, if they look and if they care.
Why is the option to include profiles there?
I think this is really intended for when you DON"t convert colors during export, as with PDF/X-4. If the colors are not yet converted, you need to know the source profile to get the destination color correct.
I don't want to give anyone the idea that it would be a mortal sin to include profiles as a matter of routine. I just want to point out that doing so MIGHT cause unexpected results in some circumstances and that it's important to know what can go wrong. Also, there is no guarantee that leaving colors unchanged and including profiles is going to get you good color on the far end. It all comes down to the skill level of the person doing the prepress.

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Ive been tearing my hair out for the best part of 14 hours trying to figure out how to keep the closest possible conversion for working with images(rgb in photoshop) right the way through a work flow until exporting to print (having used the image in Indesign). Here is the process I have been trying to get right.
1) working with RGB photo images in photoshop and converting them to CMYK (whilst holding on to as much colour as poss)
2) Importing them to Indesign and retaining the correct colours while working with them)
3) Exporting to high quality print and having all your colours stay 100% the same as you saw them within indesign.
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The problem
The problem is that there are many different colour models/profiles (both in RGB and CMYK) and each program can effect how the next one handles and stores colour. It can become frustrating knowing where to go in order to set the settings correctly as the combination of things to consider can make it confusing.
I understand many other people have similar problems and finding RGB blacks come out as grey. CMYK spaces get converted from one type to another either from one program to the next or even as things move around one program (causing all sorts of wonderful,colour errors) Plus you have imported colour profiles, working colour profiles and export profiles. All of which can interact and effect each other) So getting it all consistent is key other wise colours change and get washed out.   Especially vibrant colours like greens and blues. they fade etc.
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Since I am not an expert I wanted to post up my settings to:
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2) Other people may find them useful if they had the same problems I had,
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Save the photoshop image in CMYK by selecting:
Edit > Convert to prfile.
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select: Euroscale Coated v2   (I think this holds the colours the truest of all CMYK colour formats.)
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------ when exporting to PDF ----------
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I would like your feedback on this process, have I done something wrong / could do better? If so please let me know. I am keen to improve.

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5606 0 obj
<<
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/Subtype /Image
/Length 6
/Width 3
/Type /XObject
/BitsPerComponent 1
/Height 3
>>
stream
^Q^P^Q^P^Q^P
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3307 0 obj [/Separation /All /DeviceCMYK 4249 0 R]
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DeviceCMYK color space
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Bits per color component: 1
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That might be it, Jacob.
It's when, for instance, I have the Appearance window open and shift-click on the stroke or fill to see the color attibutes (rather than simply looking at the swatches). It kept showing up in CMYK.
But making that change in the flyout seems to have it showing properly.
Thanks!

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Do you re-print them to Adobe PDF printer using Acrobat or use distiller for this.
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Custom PDF export changes colour from CMYK to RGB!

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