I had the same issue. shiftwidth was 2 in de .vimrc but after opening vim it said 4. And this on centos and on mint with the same config it was ok. After i saw the command "verbose set shiftwidth?" i learned the option was done in /usr/share/vim/vim80/ftplugin/python.vim sp apparently this file is loaded after .vimrc (strange). The issue was also only with .py extension, i didn't notice that before. After editting this file it was ok. Best way would ben to change the sequence in which the configs are loaded i assume.