Resolution:
BW uses the antlr-2.7.5, while BE uses the antlr-2.7.7. After installing the BE, the installer put the BE classpath in the front of the original ones. So the new version antlr replace the old one. And then you got some exception when you generate the Service by process.
    The workaround is changing the classpath manually. Please move ‘;C:/tibco/be/3.0/lib/ext’ to the end of the ‘tibco.env.CUSTOM_CP_EXT’. After moving it, it looks like ‘
## this will be prepended to tibco.class.path.extended
tibco.env.CUSTOM_CP_EXT C:/tibco/be/3.0/hotfix/lib;C:/tibco/be/3.0/hotfix/lib/palettes;C:/tibco/be/3.0/hotfix/lib/ext;C:/tibco/be/3.0/lib;C:/tibco/be/3.0/lib/palettes;C:/tibco/bw/5.6/hotfix/lib;C:/tibco/bw/5.6/lib;C:/tibco/bw/5.6/lib/palettes;%TPCL_HOME%/lib/httpclient_3.0;C:/tibco/tpcl/5.5/uddi4j/lib/uddi4j.jar;C:/tibco/hawk/lib;C:/tibco/bw/plugins/lib%PSP%C:/tibco/bw/plugins/lib/palettes;%TPCL_HOME%/jviews/external;%TPCL_HOME%/jviews/6.0;C:/tibco/be/3.0/lib/ext’

Generate WebService From Process doesn't work after installing BE 3.0