If a new deployment is added to a profile via Profile.addDeployment(VFSDeployment, DeploymentPhase), a subsequent call to Profile.getModifiedDeployments() will not include that deployment. Basically, the various getModifiedDeployments() impls do a VFS scan for new content, but ignore anything that they already know about from an addDeployment(...) call.

See forum thread for more in depth discussion.