I have a Flex application with multiple modules.
When I redeploy the application I was finding that modules (which are deployed as separate swf files) were being cached
I had a similar problem, and ended up putting the SWF files in a sub-directory named as the build number. This meant that the URL to the SWF files pointed to a different location each time.
Ideally this should be catered for by the platform, but no joy there. But this works perfectly for us, and integrates very easily into our automated builds with Hudson - no complaints so far.