This week's book giveaway is in the General Computing forum. We're giving away four copies of Arduino in Action and have Martin Evans, Joshua Noble, and Jordan Hochenbaum on-line! See this thread for details.
Without further information, including how and when the employee (or employee collection) is being modified I'm not sure how we can help, although someone more familiar with Hibernate might have a better idea.
Its not Hibernate that is likely to be doing this. The query cache is pointless without a second level cache. I second David - we need to see more about what you are doing to help. Can you post your code?