Did you save the application file as Application.cfc, with capital A?
The case did not make a difference. Which is fine as it follows the normal CF patterns of the past. Any other peoples input?
Create a simple test that contains Application.cfc, test_1.cfm, and test_2.cfm. Configure the session management and create a session variable for test. Call test_1.cfm and see the output of session variable. Call test_2.cfm; and do the same thing. If you see the same values, then it has nothing to do with the server. Otherwise, server configuration issue.
We had a similar test that p. Sim described and have determined it is likely to be a server configuration issue. THANK YOU P.SIM for the input. Although not resolved we are now running down the path of troubleshooting our combination of Tomcat 6 and Coldfusion 9.
If anyone knows of any good resources in this space please do let me know.
I have two suggestions for you to try.
(1) Your problem might be caused by the session fixation issue. Pete Freitag describes this quite well in his blog, and gives you 3 possible workarounds.
(2) Use J2EE sessions instead (which you can configure in the ColdFusion Administrator).