This week's giveaway is in the EJB and other Java EE Technologies forum. We're giving away four copies of EJB 3 in Action and have Debu Panda, Reza Rahman, Ryan Cuprak, and Michael Remijan on-line! See this thread for details.
As Philip says, you need to find what Eclipse considered the "current working directory" when it launches your program. I'm not familiar with Eclipse, but in NetBeans, you can set the current working directory under Tools | Options. You should look in the Eclipse help files or browse its options in order to find what this setting is and how you can modify it.