The more information you can provide about your setup, the more likely that someone will be able to give you useful ideas. How did you set up Aggregate? Did you directly follow the documentation steps or do you have something like an existing database that you're connecting to? What are the hardware specifications of the server that you are running on, especially RAM and CPU? Can you look at RAM and CPU usage when this happens? Is there anything special about your network setup such as a proxy?
Have you read through other timeout threads such as ODK timing out during data pull?