Thank you for your post.
What version of FileMaker Server are you running? With FileMaker Server 7, when configuring the Web Publishing Engine, make sure the IP address of the host computer is a valid IP address. Do not enter the full URL. Otherwise, an HTTP 500 error occurs.
What version (and release) of Java are you running? The recommended version is Java 6 release 7. Try disabling any version higher than this.