Weblogic: No EJBs found in the ejb-jar file

When I try to deploy the Java EE project to weblogic 12c, I get the following error

No EJBs found in the ejb-jar file

However, this only happens when I deploy the EAR source folder and let weblogic compile it (split development directory). If I build the EAR first with ant and deploy it, it deploys fine.

I think the problem has something to do with the fact, that EJB module has both annotations and ejb-jar.xml descriptor present. Everything else is handled with annotations, and ejb-jar.xml just introduces the ejb-client-jar as such.

<?xml version="1.0" encoding="UTF-8"?>
<ejb-jar xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://java.sun.com/xml/ns/javaee" xmlns:ejb="http://java.sun.com/xml/ns/javaee/ejb-jar_3_0.xsd" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/ejb-jar_3_0.xsd" version="3.0">

Also, weblogic-ejb-jar.xml is used for additional configuration.

But what makes pre-built EAR and source deployment behave differently in this case and how to solve the problem? Application is using Java EE 5 and EJB 3.0.