Closing Window in Task Bar leaves app open

Ok so this may be a noob question but that would be because I'm a noob.
I have an Air application which has states some of which are invisible. There is always a systray icon where the user can close the application but in windows when the state is visible there is also a task bar icon. If the user right clicks on the task bar icon they can close the visible window but the actual application is still running (although not functioning in any way). The systray icon is still there and they can right click it to close the application but they never notice it.
This results in confusion as the application is no longer functioning but they can't resart it either.
What is the best methodology for dealing with this?
Much appreciated
Phil

I believe I've found the answer.
autoExit="true"
A function was setting it to false. Oops
Phil

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Hello,
Could be many things, we should start with this...
"Try Disk Utility
1. Insert the Mac OS X Install disc, then restart the computer while holding the C key.
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Closing Window in Task Bar leaves app open

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