I experience something similar. The flashing I see is more of a strobe light effect, in that the window flashes many times very rapidly for a split second upon opening a program window (web browser, repositories, Cinnamon settings, Home file system, etc). Most days my computer will do it all day long, and a few days it behaves itself and works as intended. Chosen theme (stock Mint X, or third party) doesn't seem to matter. Currently using 32-bit, Cinnamon, Mint 14. No idea what causes this issue. I figured it's a bug that will be fixed in a future update.
Intel i7-3770k 3.5GHz, 16GB 1600MHz RAM, 3x 1TB HDD, MSI Z77A-G45 Thunderbolt motherboard, (MSI) Nvidia GeForce GTX770, Mint 16 64-bit w/Cinnamon.
I am a n00b! Please assume zero knowledge on my part. Sorry for any dumb questions, I am still learning.