I was finally able to get our app running successfully with Apache Axis (1.2RC3) in WebSphere 5.1.0 using the PARENT LAST classloading and xerces1.4.4
These were the things I found to be necessary:
a) load all axis related jars through the EAR classloader and not web-inf/lib classloader. It seems WebSphere sometimes has conflicts with dependent classes coming throught the web app classloader.
b) edit the WebSphere\AppServer\java\jre\lib\xerces.properties and jaxp.properties. Uncomment
the lines at the bottom of both files
c) load the Apache Axis version of saaj.jar from java/jre/lib/ext
d) clean all third party jars loaded through your EAR classloader (or web-inf/lib classloader) of any javax.* and org.wc3.* SAX and DOM classes that may conflict (the xerces1.4.4.jar needs to be cleaned of this.)
-Dhananjay