At this point i'd stay away from flash plugins. I'd use HTML5 uploader instead like this one:valums uploader
Sure - you'll be able to select multiple files in modern browsers only, otherwise - it'll be file by file. but hey - if person doesn't care about upgrading to newer browsers - they really probably don't know how to Ctrl+click anyways.
Flash doesn't send cookies correctly (it sends IE cookies even if you use firefox or google chrome). So - you'll lose cookies and thus sessions. There is a workaround - to send PHPSESSID in POST requests - but it simply opens door wide open for session fixation.