Apart from what Sri has said which points to this as an InstallAnywhere issue, in the long-run you may find using the agent no installer package for the app server is a quicker option, there is a no-installer package for Tomcat
Introscope Agent Files for Apache Tomcat-No Installer r10.1
choose the one that suits your operating system
The installer does not enable Tomcat to run with our agent anyway so that manual step of updating the JVM arguments will always be there.
You just have to unzip/untar the agent archive on the machine, update the agent profile to point to your Enterprise Manager, update PPM startup scripts to load the agent and profile, by which time you may still be investigating the Windows Error 2 with no positive result.