I've been using the EAP for the past few months and never had a problem using Custom Namespaces / Manifest, configured in the Module Settings.
After upgrading to RC4 this morning, I'm now getting the following error on compile:
unknown namespace 'http://ns.mynamespace.com'
Looking through the release notes, it doesn't seem like anything in this area has changed for the Flex.
Any help would be greatly appreciated.