My sincerest apologies for resurrecting such an old thread, but I've just gone through a near-identical experience as the OP and other posters in the thread.
Long story short, I noticed some considerable noise when shooting w/ my 5D Mark III at ISO levels of 4,000. This was encountered in both dim and moderately-lit locations. Obviously, I'm aware that the images shot in dimmer areas would have more noticeable noise due to shadows and underexposing of the image. However, I Was curious as to why there was still noticeable noise in the ISO 4000 images in well lit areas (especially when compared to photos from other people).
Fearing I had a lemon, I contacted the Canon Repair Center in Chesapeake Bay, and was advised to upload my files (CR2) into Canon DPP and then compare the same image (untouched) in Adobe Lightroom 4.1, which is my standard photo processor. I did so and was completely blown away by the difference in quality. As has been said, the images in DPP featured superior noise reduction compare to those in Lightroom, which had a look of "Sandpaper" when blown up to 100%.
My question is the same as the post before mine: Is there a way to incorporate DPP into my workflow (Essentially Camera - SD Card - Lightroom - Photoshop/Publish)? I can save the images from DPP as .tif files, but when I bring them into Lightroom, I lose the ability to adjust the white balance (i.e., setting it to Flash, daylight, shade, custom, etc). I'm aware that this happens whenever you bring a tiff into Lightroom.
Alternatively, are there Lightroom settings that I can use that'll mimic the results shown in DPP? Losing total control of the white balance isn't a complete dealbreaker for me, but I'd prefer not to.
I've scoured threads here in the CR Forums and can't find an answer, sadly.
Also, I'm currently on Lightroom 4.1...does anyone know if the noise issues with the 5D Mark III have been corrected in Lightroom 4.3?
Thanks and again, my apologies for digging up old bones.