I must preface this by saying I only run boinc under linux in the background, as a "service", and do not use or want any of the GUI features.
At the command prompt, I kill boinc, download the source from one of Berkeley's BOINC mirrors using wget, chmod the file to an executable, run the script which creates a new directory, cd into it, and copy the single file, boinc to my destination directory (overwriting the existing older version). CD to the target directory, and launch boinc in the foreground, to see system messages scroll by. When assured it's working, I run it in the background and basically ignore it.
chmod 775 boinc_5.4.9_i686-pc-linux-gnu.sh
cp boinc /home/boinc/boinc
Hope this helps. Adjust paths, methods, as needed