When you install JBDS 3.0.1, you can add a runtime during the installation process. If you add an installation of EAP 5.1, it seems it is added. But when you launch JBDS, the runtime is not there. This is probably because the version 5.1 of EAP is not supported by JBDS 3.0.1. To use EAP 5.1 with JBDS you need to add the server again after installation. That is also the workaround - don't add EAP 5.1 during the installation, but add it later from JBDS.