It may have a lot more to do with your particular system than with the procedure you're using, but we can't tell. This will help us:
After Effects CS6 220.127.116.11
Windows 7 Professional, 64-bit
Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz, 3201 Mhz, 6 Core(s), 12 Logical
GeForce GTX 680 (driver version 347.52)
I have installed NVIDIA GPU Computing Toolkit 6.0 but I think there is a new version - I have no idea if that has anything to do with this but I'll update it tomorrow in any case.
looks like you have the warnings turned on in Colorista. Check your settings.
I'm not using Colorista. I've tried turning off all the effects I've added but that's not it. It does look like some sort of clipping warning though.
So when I view that rendered footage in VLC - no color noise. When I import it to AE - color noise. The only thing that makes it disappears is changing from 16 bit to 8 bit.
I'd transcode any and all DSLR footage before I ever touched it in ANY application: video editor, AE, what have you. H.264 just doesn't stand up well in the production process.
Okay, quick 'n dirty, need-this-done-in-five-minutes projects don't count. In those cases, image quality takes a back seat to speed.
Yes I did try that now (converted to DNxHD beforehand), put the footage through the same treatment and no weird effects - so perhaps that's the solution but I'm still wondering why this noise thing happened in the first place.
I've never trusted H.264 as a viable middle link in the production workflow, so I've always transcoded.
It's really stupid -- DSLR makers put great sensors and great glass in the cameras, then what do they do? They record to a codec that can't record complete information for each frame and throws away 3/4 of the color information! How dumb is that?