Thanks Roger!
Added this to the context.xml of the tomcat application
<Resource
name="jms/MyConnectionFactory"
auth="Container"
type="com.ibm.mq.jms.MQQueueConnectionFactory"
factory="com.ibm.mq.jms.MQQueueConnectionFactoryFactory"
description="JMS Queue Connection Factory for sending messages"
CCDTURL="file:///apps/install/tomcat7/shared/AMQCLCHL.TAB"
QMGR="MYQM />
Also, commented out the following two lines from setenv.sh
#export MQCHLLIB=/apps/install/tomcat7/shared
#export MQCHLTAB=AMQCLCHL.TAB
..and everything works perfectly. Thanks a lot for helping with this!