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I believe that you can change the behaviour of the application auto exiting by using 'air.NativeApplication.autoExit=false'.
However it is not altogether true to say that all applications remain open once all windows belonging to that application have been closed. For example 'System Preference' does, as does 'Network Utility' and a number of other utility applications. I guess it kind of depends on what the application does and what it's expected interactions would be.
You're right. Some apps do quit on termination of the window, but I was speaking in general. Most apps require you to quit them. This should apply to most Air apps. If this behavior can be set via "air.NativeApplication.autoExit=false", it would make more sense if Air defaulted this value depending on the platform.
I love the fact that AIR apps are closing when I hit the X under OSX. Makes much more sense for me, bcz I too often hit "x" button on a window and then need to show the dock, right click and choose 'quit' ...
While I respect your difference in opinion, it simply is inconsistent with how OS X apps behave. If Air apps are supposed to supposed to bridge the gap between desktop apps and RIAs, they need to behave like their desktop counterparts. Thus, it makes no sense for an Air app on OS X to behave like a Windows app.
This question about auto-exit behavior is a good one. I've taken the liberty of explaining why it works the way it does at http://blogs.adobe.com/simplicity/2008/09/why_air_applications_auto-exit.html as I think others may also be interested.
As for scrolling behavior, AIR can enable smooth scrolling but it can't enforce it. If Twhirl is stiff, I'd look at the application itself, first. In particular, the application may have its frame rate set on the low side.