Resolution:
If you have installed the TIBCO BusinessWorks XA Transaction Manager and then subsequently upgrade TIBCO Runtime Agent from Release 5.3 to either Release 5.4 or 5.5, you must modify the BW_HOME/bin/bwengine.tra and DESIGNER_HOME/bin/designer.tra files.

In BW_HOME/bin/bwengine.tra, find the property named tibco.env.CUSTOM_EXT_APPEND_CP and add the following to the property:

%BW_HOME%/tm/1.0/etc;%BW_HOME%/tm/1.0/lib;%BW_HOME%/tm/1.0/lib/ext

In DESIGNER_HOME/bin/designer.tra, find the property named tibco.env.CUSTOM_CP_EXT and add the following to the property:

%BW_HOME%/tm/1.0/etc;%BW_HOME%/tm/1.0/lib;%BW_HOME%/tm/1.0/lib/ext