There is no explanation as to why Jenova chose THAT time to escape.
Maybe it has something to do with what Sephiroth said on the boat - "The time is now"? Maybe Jenova's head controls all of the cells, and thus when her body is sealed in Midgar she can still control the body. Hence she decided to leave it dormant for 5 years? It's possible. And the first sign of her cells may have been Cloud's.