This is an odd problem.
I’'m running on a fresh install of Vista x64, and have the Java6 environment running. Whenever Spark is running, the other elements of the Aero interface are unusable. e.g. I can click into windows and nothing happens with them. The rest of the items retain their position and presence on the screen, but they stop updating and appear to be frozen for all intents and purposes. The condition goes away as soon as Spark is closed.
The way I resolve the matter is to log out, and then re-log in.
The problem is consistent in the online and bundled JRE installers. The Java6 I used with the online installer comes straight from Sun. My video hardware is a Nvidia GTS 8800, with the latest ForceWare drivers as of yesterday.