Original .pdfs colours different (darker) in printed magazine - WHY?

I am running InDesign on a PC (Windows XP). I use it to edit and design a full colour short run magazine which is professionally printed. My problem is that the colours of the final printers proofs and finished magazine are coming through darker in tone, particularly the reds and blues, than the .pdfs I generate using InDesign. On my screen and on the HP printer I use to run off test pages, the .pdfs colours are fine. Somehow the printers' equipment and/or software is making them darker on the final printed magazine, unacceptably so this time.
We generate the magazine using InDesign and send the final .pdfs to the printers via an ftp server service (YouSendIt).  The printers then create the final proofs for me to approve and sign off. Sometimes they send me these in the post as printed sheets (sherpas) to sign off. Recently I have been going online to their "Delano" server and approve the proofs on line. Last time round however they had a problem with it and sent me the printed proofs to sign off.
Most of the images we used originate as digital ones and are supplied to us as high res. Occasionally there is a scan. However as the printer uses cmyk images, and insists we convert any rgb images to cmyk before they will process our .pdfs. We do the picture conversion from rgb to cmyk using Photo-paint.
In the past I have had problems with the colour balance of the final proofs being darker than my original .pdfs.  Changing colour balance at the pre-press stage is expensive and as it is just about acceptable if the final magazine does not contain too many photos with a lot of grass and sky, then I will let it run.
But it has happened again and is unacceptable. I was sent a very good quality professional photo for the cover (in high res digital format) taken outdoors on a sunny day with a lot of grass and it has inevitably printed too dark on the final cover. (sky is greyish not blue and  grass is orange-ish not light green). Same problem throughout.
The printed proofs supplied by the printers this time were too dark, so I phoned up the Production Manager to tell him this before I signed them off. He said not to worry as they were not 100% accurate for colour anyway. To be on the safe side, I marked on all the proofs individually that the colour was too dark, and printed out and sent them a .pdf of the cover, showing the correct colour balance.
Still the printed magazine arrived too dark, just as it was on their proofs. I again complained to the Production Control Manager who put me onto their Technical Support guy, who is not very helpful (always looks at it being customers fault as his first position). He said first of all that it must be my scanning, and conversion from rgb to cmyk. I pointed out the cover photo was not scanned but an original high res digital image supplied by a press agency. So he then said my PC and printer must be at fault.
I have gone back and looked at the colours on previous issues and they are all on the dark side, for example bright blue skies come out greyish, but it only really notices if there is a lot of grass and sky in the pictures. Is the printers software or equipment attempting to compensate for needing extra colour in some way? Also they are primarily a MAC house and I use a PC. Could this affect the colour calibrations?
I need to talk to them again but want to do so from a position of knowing something about how a .pdf gets converted into a final proof and how the colours could get darker, given their tech support is unhelpful.
If it is relevant, this is their printing equipment: Twin Computer-to-Plate lines; Two Heidelberg 8 colour presses .
Any advice anyone can give on what might be causing the final magazine to be darker in tone than my InDesign .pdfs would be appreciated.

Wow – thanks for all your suggestions I am going to have to take a while to digest and try them out and report back.
I am in fact on very good terms with the Production Manager at the printers but I think he has rather been dropped in it, as it seems the unhelpful tech support guy has just left and not been replaced so the Production Control Manager is left trying to sort out advanced technical aspects of prepress for which he has not been trained.
I have to ask why the printers don't give you the information you need up front instead of claiming a .pdf from Indesign is all it takes.
In all this .pdf fine tuning stuff I am reminded of my earlier career in IT. I was involved in setting up an early wide area VOIP network (Voice over Internet Protocol  - a sort of Skype to the uninitiated). To make this work we needed a digital switchboard which was configured to the latest European standard and software to match. Everyone assured me that the protocol concerned (let us call it 802.11) was brand new and had not yet had time to develop any variations……of course there were all sorts of problems not least that the line kept dropping and everytime it restarted we got charged a reconnection charge. I won’t bore you with how we got there in the end but needless to say, one man’s VOIP implementation of VOIP using 802.11 is not necessarily another’s.
I am reminded of this in all the issues surrounding exporting .pdfs to get the correct colour balance in the resulting publication. I swear to you this was never mentioned to me as being an issue at any time by anyone when we started down this route.
Meanwhile today I asked the printers’ salesman chasing my business to send their technical spec – pointing out I work on a PC running XP - and this is what I got
A sheet headed “Recommended settings for creating a PDF/X directly from Adobe InDesign CS3. This example was created on Mac OS x 10.5 using InDesign 5.0.1”  This is followed by a series of screen prints with the following headings
Check your Transparency Flattener Preset is correctly configured (via the edit menu) this will be selected in the Advanced tab (step 6)
Select File – Export then in Format chose Adobe PDF and name the file, select folder to save it to and click Save
In General select single page to print set compatibility to Acrobat 4 (PDF 1.3) and deselect all the list Options and include checkboxes
The Compression tab sets the options for how the PDF will handle resolutions for placed colour, grey scale and monochrome images
The Printers marks should be enabled as below.
Use the Destination and Output Intent profile name relevant to the publication. ISO Coated V2 300 is used here as an example only.
Ensure there are only process colour and no Spot colours. Converting colour to CMYK at the PDF creation stage can give unpredictable results
Select the transparency Flattener previously created. OPI should be disabled. Here is also where you can opt to create a JDF file
Make sure all the options in Security are disabled. Summary lists all the settings that can be applied it can be saved as a text file for reference
Note item 6 – it does not actually tell me what the printers recommended settings for my publication are
And Note also item 7 where it says that converting to colour to CMYK at the PDF creation stage can give unpredictable results

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