So I started running into this problem last night. Any photos hat have particularly bright spots, or a large contrast range form these patches of pure red, green or blue. It seems like red forms wherever the photos approach 'near-white', blue where it is 'near black', and I have yet to determine what causes the green (it is far less common). But this is across all of my photos. Even the old ones that I know are alright - have gone to print and have not been adjusted since. But this only happens when viewing the photo in develop mode, in library mode the photos always display correctly. I've attached images to demonstrate.
I don't know if you can see in the develop image, but the front grill is speckled with blue pixels, as well as inside the wheel hubs, this car's windshield, and on the windshield of the left-most car across the street. If I drop the exposure, the blue speckling becomes more prevalent (red splotches shrink). If I increase it, the red splotches grow (blue speckling decreases). This happens with daytime photos as well, but usually just with the reds, and occasionally the greens. I've yet to run into green splotches on a nighttime photo.
I use a Nikon D7100 exclusively at the moment. I always import to my computer using Lightroom's tool. I am on Windows 8.1 64-bit, using an nVidia (EVGA) GTX 760, 16Gb of ram, an Intel Core i7 3770k. I've already done a clean reinstall of my graphics drivers, but I stopped short of a Lightroom reinstall. The NEFs themselves display perfectly inside of Irfanview 4.36. I wanted to test to see if it was a general Adobe issue, or just Lightroom, but I also discovered that my PS CS4 is now refusing to open NEFs - "Could not complete your request because it is not the right kind of document". This could be a separate issue, or it might be related because they started happening at the same time - never had a problem opening an NEF from my D7100 in photoshop, but it's been a couple months since I've last had to go into photoshop to do editing for a shot.
The only other change I can think of is I ditched my second monitor in a recent move. But that one was my secondary monitor, going through a DVI-VGA adapter. It was old, flickered a little when displaying a darker image, and I'm pretty sure it's reds never displayed correctly. It was never used for anything more than hosting a library grid. And yes, I've checked my calibration of my monitor 24" Asus. The exact model number escapes me at the moment (ASUS isn't the best at labeling model numbers on their product), but it's a few years old.
You have the clipping indicators activated, red for highlight clipping and blue for shadow clipping.
Click the little triangles at the dark and light ends of the histogram to toggle the clipping warnings on and off.
I feel like a freaking idiot now. That was it. I don't recall turning them on - but I glad you caught it this quickly. I was just about to reinstall Lightroom (after rolling back through 3 generations of graphics drivers, with no luck).
If you are clicking around in LR and turn them on with an image that doesn't have any clipping then nothing seems to change and you might leave them on, and then be confused when there is an image that has clipping.