I just came across this problem during an upgrade from Windchill 9.0 M070 to Windchill 10.2 M030.
Removing the following property from site.xconf and propagating the change with the command xconfmanager -p from a Windchill shell solved it for me.
<Property name="wt.homepage.jsp" overridable="true" targetFile="codebase/wt.properties"
value="$(wt.server.codebase)/servlet/Navigation"/>
Remember to restart the method server to let the change come into effect.