Obviously you have to remove all redundant newlines in xdoclet-build.xml in order to make the ant-target(s) do an appropriate job. Quite weird with respect to the fact that the ide itself creates the config file(s) on which it does not work always correctly. Showing that the build is finished without errors and failing to insert values in the config file is a little bit deceiving.
I also sometimes encountered the problem that updates to the xdoclet settings via the ide are not transferred to the config file. So delete the configs and let the ide generate 'em again.