I don't get any of the wireframes showing on any of the 4 different systems I am running so before I can help I think we need to know your OS version, system specifications including your GPU specs, and something about your composition. The only thing that I think can possibly be going on is that you had wire frames turned on and that you have some cache issues. Try purging your cache.
In addition to what Rick asked, what third-party effects are you using in your comp?
OS: Windows 7 64bit
CPU: Intel Core i7-3930 @3.2GHz
GPU: Quadro 600
HDD: Intel SSD
I am not using any 3rd party effects. I just get the flashing of the underlying wireframes when the comp gets heavy. That is to say, there are more than 3 layers. The wireframe flashes when the comp is processing, then disappears. I have tried purging the cache - but this has not fixed the problem. The only way I have been able to prevent it it by turning 'Handles' off in 'View Settings'. This does have the negative side-effect of making it hard to tell what objects you have selected at any time. Using 'Fast Draft' also prevents the wireframe flashing.
Thanks for the help.
4 layers is hardly a heavy comp.
Does this happen even if you have something simple like four layers of the same 100x100 solid?
Have you tried updating the driver for your GPU?
I have tried updating to the latest drivers - but this has had no obvious effect. By heavy comp I really mean one that takes more than 1 second to process the frame. The scenes where the flashing is the worst is when I am loading frames from an image sequence, or when there are multiple transformations to the layers (levels, masking, color grading). A simple scene with multiple solid layers renders in an instant, so there is no flashing. But once the render time for each frame goes up >1sec, this flashing occurs each time i move to another frame. When scrubbing through a sequence, this flashing gets very distracting.
That's really odd. It certainly seems like something is awry with your GPU and OS communication via AE, but this is really outside of my area. Hopefully Mylenium or one of the Adobe guys can take a look.