I'm having no problems submitting AIR files now but while submitting a file to the Flex category today it errored out looking for an included .fla file in the ZIP. I ended up submitting it with a fake .fla included for now (to bypass the error) but wanted to mention that I would expect most Flex submissions would include MXML (Flex source) as opposed to .fla (Flash)

Thanks for putting up with my constant demands BTW