"I installed a new version of Extension Manager, but it did not migrate my extensions when it was launched. Those extensions were installed in previous version of Extension Manager."
Extension Manager can migrate extensions installed in previous version of Extension Manager, but it only handles the latest previous version. For example, Extension Manager CS6 can migrate extensions installed in Extension Manager CS5.5, but not Extension Manager CS5. All extensions that were migrated will be in "disabled" state in Extension Manager, and you can enable them later. For pre-installed extensions like some extensions in InDesign or Fireworks, they will not be migrated because it is unnecessary.
You can remove the file named "Migrated.YES" in the folder below to migrate extensions again.
Windows( EM CS5.5 and earlier ):"C:\Users\<UserName>\AppData\Roaming\Adobe\Extension Manager CS\Configuration\Extensions\"
Windows( EM CS6 ):"C:\Users\<UserName>\AppData\Roaming\Adobe\Extension Manager CS6\EM Store\"