Amaya 11.3.1 has some bugs, the supposedly bug fixing cvs version ..
http://www.w3.org/Amaya/User/cvs.html : I saw no difference.
Luckily the best behavior is on Ubuntu 9.04 ..
Some issues on other Linux.
sudo apt-get install libcppunit-dev libglu1-mesa-dev \
libgl1-mesa-dev librdf0-dev librasqal1-dev libraptor1-dev
cd Amaya11.3.1/Amaya/ && mkdir build && cd build/ &&
../configure --with-libwww=../../libwww/libwww-config --enable-system-raptor
&& make all && sudo make install
.. And the command amaya displays a nice GUI.
..
This link is referred to in the Ubuntu Forum ..
http://www.w3.org/Amaya/User/Autoconf.html#L437
.....