Do you have <Automatically write changes into XMP> checked in the Metadata tab of Catalog Settings?
Are the images that you are editing when this happens Raw images or are they TIFFs, PSDs?
I observe this behavior with TIffs and PSDs when <automatically write changes into XMP> is checked. It seems that in that case Lr is reloading the image with every change done in the Develop Module and that reloading of the image causes a short flicker of the screen, i.e. the image disappears and reappears.
I have observed this behavior since Lr 3.
It disappears when you uncheck <Automatically write changes into XMP>.
At this point, I think I will have to go back to LR 3.x. Lightroom 4 is so unstable that I cannot get it to work. I constantly get not responding messages and screen flickering in the develop module.
I have done everything I can find and nothing seems to work. It is either an incompatibility with the AMD video drivers (best guess) or there is something seriously wrong with the code (second guess), however LR 3.2 does not have this issue.
Lightroom version: 4.2 RC 
Operating system: Windows 7 Home Premium Edition
Version: 6.1 
Application architecture: x64
System architecture: x64
Physical processor count: 6
Processor speed: 2.8 GHz
Built-in memory: 16381.5 MB
Real memory available to Lightroom: 16381.5 MB
Real memory used by Lightroom: 603.5 MB (3.6%)
Virtual memory used by Lightroom: 621.6 MB
Memory cache size: 191.8 MB
System DPI setting: 96 DPI
Desktop composition enabled: Yes
Displays: 1) 1920x1080, 2) 1280x1024
Your computer maxing out all cores while working with Develop is entirely normal. Flickering has been reported with TIFF files coming back from PS when automatically write to xmp is turned on. I don't remember any other reports of it happening to raw files, so there's could be more to investigate here but it doesn't appear to be a widespread issue.
I'd guess you may be right about the graphics interaction, so a couple more questions for you:
1. You have 2 monitors attached - does it happen with only 1?
2. Have you tried updating your video drivers - or rolling back to an earlier version?
3. Which graphics card?
4. Which bit of the screen is flickering?
1: No, happens on both.
2: Yes. Updated, rolled back, updated again. AMD Video Drivers.
3: AMD Radeion 5570HD X 2 in Crossfire.
4: The frame containing Lightroom. Other frames do not flicker. (It could be an Explorer issue, but I'd think it would do all of them.)
5: When the flickering starts, the computer locks and the CPU maxes out.
I'll try full screen and see if that stops it.
I will unplug the other monitor tonight and see how that goes.
It is the whole LR window.
It happens when:
The image is resolving on the screen
I move from module to module
I move a slide-bar or make a change in the develop module
an image is importing and I am viewing other images at full screen
I am sure there are some more actions that cause it I just can't remember them just now. I will play with it some more this evening.
This is really all I could find on this issue with google. I have the same problem, off and on but it makes it impossible to work. When I used to just use elements it happened with elements often as well. Never with any other program and only the adobe program flickers. Now I am using CC and lightroom flickers like crazy, especially when I try to use an adjustment brush or the clone tool. I also have a serious issue with the adjustment brush doing nothing at all. I can select it, I can move it around and it won't do anything. Turn on the show mask option and it doesn't even apply. Occasionally I can work on other photos, come back to it, try a different brush first and then try the one I want and it will work but more recently it is completely unresponsive. Right now I can't even work with the flickering though. I have my task manager open and it is not using all of my CPU when it does it. It's just bugging out like crazy. I restarted LR, I restarted windows- still doing it. Then it will go away for days or weeks and then come back for days in a row. How is this possible?