MQ Explorer stops displaying most information - ibm-mq

Question

After using MQ Explorer 7.5 on Ubuntu 12 to add JMS Connection factories and a JMS Destination it decided to stop displaying my two queues and subsidiary info as well as the new JMS information. I tried a few things to get it to work again: stopping the queue manager/restarting, rebooting etc. even reinstalling MQ Explorer without any luck.
I can do a status on the "empty" queues folder and it then shows me my two queues; each has "queue monitoring" set as off. Is this relevant? Can I set it on ?
Am I stuck with MQ Explorer to display and manage the JMS objects (there doesn't seem to be any documentation about how to use the command line for JMS objects) ?
more detail:
so I created objects using the following:
DEFINE QLOCAL (QUEUE_FROM)
DEFINE QLOCAL (QUEUE_TO)
SET AUTHREC PROFILE(QUEUE_FROM) OBJTYPE(QUEUE) PRINCIPAL('bsmith') AUTHADD(PUT,GET)
SET AUTHREC PROFILE(QUEUE_TO) OBJTYPE(QUEUE) PRINCIPAL('bsmith') AUTHADD(PUT,GET)
SET AUTHREC OBJTYPE(QMGR) PRINCIPAL('bsmith') AUTHADD(CONNECT)
DEFINE CHANNEL (CHANNEL1) CHLTYPE (SVRCONN) TRPTYPE (TCP)
SET CHLAUTH(CHANNEL1) TYPE(ADDRESSMAP) ADDRESS('127.0.0.1') MCAUSER('bsmith')
DEFINE LISTENER (LISTENER1) TRPTYPE (TCP) CONTROL (QMGR) PORT (1415)
START LISTENER (LISTENER1)
So these were all visible then in MQ Explorer using a user that was part of group mqm.
I then added, using MQ Explorer, a file based JMS context, two JMS Connection Factories, and a JMS Destination. After adding the JMS Destination the MQ Explorer stopped displaying everything except the Queue Manager and the JMS context in the MQ Explorer UI.
if I try to start the LISTENER again using the command START LISTENER (LISTENER1) it will tell me that it is already started. When I add a new queue to the queue manager using a command it also is not visible on the UI. A refresh doesn't change this.
/etc/environment is set to:
export JAVA_HOME=/usr/lib/jvm/jdk1.6.0_45
export MQSERVER="SWI_CHANNEL/TCP/COM22189(1415)"
export MQ_JAVA_LIB_PATH=/opt/mqm/java/lib64
export MQ_JAVA_INSTALL_PATH=/opt/mqm/java
export MQ_JAVA_DATA_PATH=/var/mqm
export LD_LIBRARY_PATH=/opt/mqm/java/lib64
CLASSPATH=.:/opt/mqm/java/lib/com.ibm.mq.jar:/opt/mqm/java/lib/com.ibm.mqjms.jar:/opt/mqm/samp/wmqjava/samples:/opt/mqm/samp/jms/samples:${JAVA_HOME}:${MQ_JAVA_LIB_PATH}:${CLASSPATH}
PATH=".:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:${JAVA_HOME}/bin:${JAVA_HOME}:/usr/lib/jvm/jdk1.6.0_45/jre/bin:${MQ_JAVA_LIB_PATH}"
trying the JMS Admin tool suggested gives :
/opt/mqm/java/bin$ ./JMSAdmin -v
Licensed Materials - Property of IBM 5724-H72, 5655-R36, 5724-L26,
5655-L82 (c) Copyright IBM Corp. 2008, 2011 All Rights Reserved. US
Government Users Restricted Rights - Use, duplication or disclosure
restricted by GSA ADP Schedule Contract with IBM Corp. Starting
WebSphere MQ classes for Java(tm) Message Service Administration
Initializing JNDI Context... INITIAL_CONTEXT_FACTORY:
com.sun.jndi.fscontext.RefFSContextFactory PROVIDER_URL:
file:/C:/JNDI-Directory JNDI initialization failed, please check your
JNDI settings and service. The name '"/C:/JNDI-Directory"' cannot be
resolved
Error: javax.naming.NameNotFoundException; remaining name
'"/C:/JNDI-Directory"

Answer 1

The error Error: javax.naming.NameNotFoundException; remaining name '"/C:/JNDI-Directory" can be resolved by creating a folder named JNDI-DIRECTORY in C drive. This is the place where .bindings file will get generated.