Start by confirming that the same ColdFusion mappings exist between the old and new servers.
Secondly, are the web roots set up the same since CF first tries to resolve CFC paths relative to the web root?
Can you give us an example of a CFC that cannot be found (i.e. coldbox.system.plugin) and then show us where that file does exist in regards to the web root of the application, as well as any application-specific mappings, and ColdFusion server mappings?
I doubt your issue is directly related to Apache, since CFC resolution all happens in the CF server, which Apache has no knowledge of.