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These sound like they may be asl related issues. If you are running OS31, you should be using the latest asl.js from the new version of the toolkit.
I'm assuming you have the programmers guide, but I'll add a link here in case someone needs it.
When you load your initial page, are you trying to initialize the scanner and set the callback function right on the page? If so, you may be doing it before asl has fully loaded. You may need to subscribe to the loaded event and put that code in there so it executes after asl has initialized.
scanner init code here.....
On question 2, how are you calling the FTP app? I think you will want to use asl.run.