That's definitely odd. You're saying "make install" is updating portions of Sigil in locations other than /usr/local/ (the default prefix if following the directions)? If that's the case, I recommend doing a purge of any and all Sigil files and starting the configure/build process over again.
sudo apt-get remove sigil
(will remove any repository installed version of Sigil)
If you custom-built Sigil v0.9.8 with the default prefix (/usr/local) you will need to remove the following files/directories (adjust accordingly if you specified a different prefix):
/usr/local/bin/sigil (the launch script)
/usr/local/share/pixmaps/sigil.png (the sigil icon file)
/usr/local/share/applications/sigil.desktop (the xdg desktop file)
/usr/local/share/sigil/ (the sigil support directory)
/usr/local/lib/sigil/ (directory that contains the sigil binary and third-party libraries)
NOTE: that's three files and two directories to be removed.
Empty the build directory you used to build Sigil in and start over with the cmake command (make note of which Python version the cmake configuration finds. If it's not 3.6.3, we may need to do some tweaking).
I have some family coming in this weekend so I may not be able to respond as quickly or as often as is necessary, but I'll be back. I'm not giving up.
