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I have a PMR open - so far their lone suggestion (to a known problem) has
not helped.

Additionally, verify the PTFs si27813 & si27814 are applied.

Thay are.

What does the following request show?:
wrklnk '/qibm/proddata/HTTPA/LWI/*' /* output & a ? follow */
Object link Type
apps DIR
conf DIR
runtime DIR
security DIR
-- Or is there also the following DIR?:
plugins DIR

There is no plugins DIR but other than that it matches what you have above.

The following may be of interest:
dspf '/qibm/proddata/HTTPA/LWI/conf/overrides/config.properties'

....+....1....+....2....+....3....+....4....+....5....+....6....+....7....+.
...8....+....9....+....0....
************Beginning of data**************
com.ibm.lwi.jaas.additionalConfigDir=
com.ibm.pvc.webcontainer.port=2002
com.ibm.pvc.webcontainer.vhost.configfile=/QIBM/UserData/HTTPA/LWI/conf/virt
ualhost.properties
java.security.auth.login.config=
osgi.framework=file:/QIBM/ProdData/HTTPA/LWI/runtime/base/eclipse/plugins/or
g.eclipse.osgi_3.0.1.0-WED01
osgi.configuration.area=file:/QIBM/UserData/HTTPA/LWI/conf/
osgi.install.area=file:/QIBM/ProdData/HTTPA/LWI/runtime/base/eclipse/
osgi.instance.area=file:/QIBM/UserData/HTTPA/LWI/runtime/base/workspace/
osgi.logfile=/QIBM/UserData/HTTPA/LWI/logs/lwi.log
rcp.data=/QIBM/UserData/HTTPA/LWI/
cp.home=/QIBM/ProdData/HTTPA/LWI/runtime/base
-data=/QIBM/UserData/HTTPA/LWI/runtime/base/workspace
com.ibm.pvc.webcontainer.port.secure=
com.ibm.pvc.webcontainer.encoding.configfile=/QIBM/ProdData/os/osgi/LWI60/co
nf/encoding.properties
************End of Data********************

dspf '/qibm/userdata/HTTPA/LWI/version.properties'

....+....1....+....2....+....3....+....4....+
************Beginning of data**************
com.ibm.lwi.buildversion=6.0.1.0
com.ibm.lwi.builddate=20060831
com.ibm.lwi.buildlevel=0635A_53lwi601
************End of Data********************


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