Description:
After running the JIRA installer, the application will not run from the Start menu.

Cause:
The 'service.bat' file in version 4.0 has the default service name set to JIRA300410144737 (lines 43 to 45) as seen here:
rem Set default Service name
set SERVICE_NAME=JIRA300410144737
set PR_DISPLAYNAME=Atlassian JIRA 4.0

while version 4.1.1, has it set to Tomcat6 which is what caused this whole (tiny) mess (lines 58 to 60):
rem Set default Service name
set SERVICE_NAME=Tomcat6
set PR_DISPLAYNAME=Atlassian JIRA 4.1.1 6

This settings might cause problems when you try to install JIRA as service if you already have a service with the name Tomcat6 installed on your system.

Workaround
Start and stop the service directly from the service menu.

To get the start menu working correctly:

1. Look at the service name. Right-click the service and choose properties. Notice it's Tomcat6.
2. Change <jira-install>/start_service.bat to net start Tomcat6

If you also have a service called Tomcat6, you can change the service name in service.bat, uninstall and reinstall the service. See http://confluence.atlassian.com/display/JIRA/Running+JIRA+Standalone+as+a+Service for how to uninstall and reinstall the service.