Starting in 6.03, iSeries started supporting multi-versions of Domino running on the same machine. To enable this, the executables had to be installed in separate libraries. e.g. for 6.03, the library is QDOMINO603. Therefore the solution of having QNOTES in the library list will no longer work. You should be able to set the LIBPATH environment variable (or pass it on the java command line invocation), so the executables can be found. If you never intended to install more than one version of Domino on your iSeries machine, LIBPATH should be set to '/qibm/proddata/lotus/notes'. This will be a symbolic link pointing to the latest installed version of Domino on the machine, which will be 6.03 in this case.
Info on setting LIBPATH: http://publib.boulder.ibm.com/iseries/v5r2/ic2924/index.htm?info/rzaha/jni.htm
. Info on Domino multi-versioning on iSeries: http://www-1.ibm.com/servers/eserver/iseries/domino/mv/