I think I just figured out why there is such a time slowdown during certain puzzles. Today, for example, for one cryptogram I waited almost 20 seconds before I could enter any letters, and have been noticing that when the ads include animations (Flash?) the screen updating freezes until the animation downloads. Other times I will try to get the focus for a letter and have to wait about 5 seconds or more.
Has anyone else noticed this or is it just my computer?