This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
I don't believe there's any max as far as Java is concerned, other than Integer.MAX_VALUE which limits the size of any array. Perhaps there's some platform limitation? What exactly happens when this method fails? Is an exception thrown? What if you list files outisde Java, using OS commands - can you list all 1000 files? You can probably list the files to a new file - e.g. (for Windows) (Don't put the new output file in the same directory you're trying to list - that just confuses things.) Once you have the output in a file, you can see how many lines there are, and check for any other anomalies.