First step is to make sure the app is running without security enabled. This way you know the problem is somewhere in the security settings. If it does not run without the security you have to fix this problem first.
Does the URL you use to start the application contain '.jspx'? in this case you are only starting the page but not the workflow.
Open the view controllers project properties and select the run/debug/profile node. Open it and select the default run configuration and edit it. Set the 'Default run Target to your adfc-config.xml, uncheck the 'Attempt to run active file before ...' and then select the 'ADF Task Flow' node. Here you select your welcome page.
Now click the run or debug icon in hte button bar under the menu in jdev.
See if this helps. If not post the url you use to start the app.