What are you running the make install on?
Without trying not 100% but I believe handbrake and hblib are done at 'make'
Then you would build the gkt gui and that would be installed with a 'sudo make install'
Edit: built a couple of times, seems to be a couple of ways, either with 'make' or './configure && jam'
when that's done
At this point 'make 'installs to /usr/local, to change to /usr then,
cd gtk && ./autogen.sh
./configure --prefix=/usr && make
And then either
sudo make install, or (red to just make the .deb
Make sure you give it a new version number in checkinstall (name, comments, ect. if wanted
sudo checkinstall --fstrans=no --install=no