Could be bad for your situation, but the only way I have successfully gotten around some of the issues you're describing is by outputtings static html files and opening in the user's local browser.
In your case that could be a large amount of code and you also have issues with whatever local browser they're using. (God forbid they have IE then you'll be outputting your html / canvas and it still won't print.)
Unfortunately I don't really have an answer for you and I don't think Adobe does yet. (You can see my basic workaround for printing to the user's local browser here: http://vfoo.wordpress.com/2009/03/24/adobe-air-print-css-and-html-printing-hack/ Note: I don't think my workaround will be the best for your because relying on the user's browser for canvas printing is a bit of Russian Roulette)
To request better printing features as well as describe your issues to Adobe go here: