Hi, I don't use Flash but I reckon there is a problem/issue with Flash in QT after QT 7.1.3. or thereabouts...?!
Automator is great but so far I have only found 'QT' Actions within Automator (for moving image stuff) which means Flash conversion probably isn't supported as it is a problem from within QT itself - someone can put me right here, I'm bordering on 'out of my depth'.
More usefully -
This -
http://www.flash-on-tv.com/flash-to-video.html - may be $40 well spent as it seems to support batch Flash to .mov conversion, haven't tried it but just Googled it for you.
I found it on this Blog
http://videos-flash.blogspot.com/ which looks useful.
I initially thought
http://www.ffmpegx.com/index.html may be able to help you but it looks not.
Automator
I am starting to enjoy Automator. If you haven't tried it yet give it a go.
I can't programme but have made a couple of Automator actions to batch rotate still images 90 degrees left or right, which is always a pain in the workshops I run, it saves the originals to a seperate file, takes just a second and is available as an Automator plug-in right-click from Finder anytime - wicked.
Also I have an Automator plug-in to find .movs with key words in the titles and then display the result in Safari which can be paged through.
There are various Automator actions
http://www.apple.com/downloads/macosx/automator/
available for free or share from Apple. there are some realy useful freeware Photoshop Actions here.
I blogged some stuff about Automator. Nothing that isn't in this post-
http://moongold.me.uk/moonblog/2007/1/3 ... ssing.html
Hope that helps - Enjoy -