I run 64bit Java on a 64 bit Win8.1 machine and I too have been having issues testing Java Applications after I upgraded from Java 51 --> Java 55.
Everything was working until I upgraded Java.
We finally got it to work today when we made a change to the Project Suite Properties
Double click on the Project name and in the Workspace select the Project. Open the Properties tab and select Open Applications>UI Automation and check (or add) the "List of accepted windows" checkBox
