Without knowing any details about the application, what it does, disk subsystem, RAM, type of processor(s), hardware config, OS version, data storage and access techniques it is a bit difficult to say what the source of the problem is.
Has this application been run on a single cpu box before? If so I'm guessing it seemed to be faster - however what metrics are you using to determine performance? Are you doing any logging / performance monitoring? Has any other details changed?