There are things that can pin a module in memory. Styles have been address in Flex 4.0. Resource have been addressed in Flex 4.5.
You will also want to use the profiler check for leaks in your own code.
Are you using Spark Modules or Halo Modules?
How are you skinning the modules?
We are using the <mx:Module>..I didn't know there was a spark module. Also we are using Flex 4.1
The components within the module are being skinned like this:
<s:SkinnableContainer skinClass="skins.whiteContainer" height="100%" width="40%">
The Spark Module is new for the upcoming Flex 4.5 release.
Here's a link to ways modules can be pinned in memory: http://blogs.adobe.com/aharui/2009/08/what_we_know_about_unloading_m.html
As I mentioned before, Styles have been address in Flex 4.0. Resource have been addressed in Flex 4.5.