If I had to guess I'd bet you use JSP (Java Server Pages) and don't precompile them (very naughty) which means that each page must be compiled first. Without knowing more about the specifics of your application (like what forms of caching it uses and where), I cannot say for sure.
Thanks for the input, we are not precompiling our jsp files during our release. What do you think would be the best way to do that? Is there a we can precompile these jsp's without including the compiled class files in our ear. We would prefer that the precompilation occurs when we start our jboss server.
Thanks for all your help.