Icons in dock become semi-transparent and black boxes appear when using chrome/flash

[super!]

When using flash player inside chrome, after a while the dock icons become semi-transparent and sometimes a black box will appear on the desktop. With regards to the black box, It stays behind all windows (I can hover a window over it to hide it) and it only remains on the desktop wallpaper. Once I stop using flash player, the dock returns back to normal, but I have to switch wallpapers for the black box to disappear. I haven't noticed it with Safari, but it's possible that it could still occur with extended use.

I've tried installing a fresh copy of Mountain Lion but the same thing happens. I also ran a hardware test which showed no issues. Could this be down to software (flash)?

 

[Saturn1217]

Yikes!

That looks horrible. Sorry I can't help you but I use chrome and flash on a regular basis and I've never seen that.

Maybe your dock preferences are corrupted. You might try deleting them and then going into terminal and typing "killall Dock" (it will restart your dock).

When you reinstalled mountain lion did you do a true clean install (no migration what so ever. reinstall all apps manually? Use drag and drop to move files). I only ask because after migrating from my old MBP to my new MBA I noticed that even though I unchecked migrate settings some settings still got migrated over from the old computer.

I hope you get that sorted!