There could be two reasons why this is happening.
a) The ESB RT and BPEL are running in separate OC4J containers. If they are, BPEL processes do not get auto-registered in ESB.
b) You had applied a 10.1.3.3 patch, and hadnt backed up your oc4j-ra files. In this case, when the patch is applied, the oc4j-ra files get overwritten with default contents, and the Topic Connection Factories that get used to propagate BPEL process metadata into ESB at deployment time go missing. Hence make sure that you backup all your oc4j-ra.xml files before applying the patch, and restore all of them after applying the patch. On the whole, read the 10.1.3.3 patchset notes carefully before applying the patch.