What a pain in the arse this was… reinstalled CS4 design premium twice to try and resolve but everytime I opened up an Adobe CS3 or CS4 file the Flash would unexpectedly quit. If I tried opening Flash CS4 first then opening the file, Flash would just hang and become non responsive.
It turns out the solution is quite simple, but perhaps time consuming. After reading http://jobemakar.wordpress.com/2008/10/18/how-to-crash-flash-cs4-with-a-single-click/ I attempted the suggested fix of looking for corrupt fonts. Actually, I skipped the looking part and removed all the fonts from my fonts folder that Windows would allow me, then added the fonts from a work mates PC. All working happily now, the migration from CS3 to CS4 is complete.