The class has the following code:
IPath soapDeployPath = rtHome.append(SOAP_AS_LOCATION).append("server").append("default").append("deploy");
IPath deployPath = rtHome.append("server").append("default").append("deploy");

These are incorrect if the runtime configuration is not default or if some other preferences have been set to change the location. You should instead adapt the IRuntime into a IJBossServerRuntime (if possible) and then call getConfigurationFullPath().append(IJBossRuntimeResourceConstants.DEPLOY);

Also the same class has the following if statement twice:

if (!esbPath.toFile().exists() || !sarPath.toFile().exists())

{ esbPath = libPath.append(JBOSSESB_ESB); sarPath = libPath.append(JBOSSESB_SAR); }

if (!esbPath.toFile().exists() || !sarPath.toFile().exists())

{ esbPath = soapDeployPath.append(JBOSSESB_ESB); sarPath = soapDeployPath.append(JBOSSESB_SAR); }