Hi,
there is possibly a bug with the way the "Default compiler" option works in the "Build" menu in the application options.
Description
You can click a dropdown list where you can select one of a few compilers. Next to the dropdown, there is a "wrench" button that opens up a dialog titled "Quick Build Command".
In this dialog, it would seem that you have the option to customize the steps taken for the default compiler. You can add steps like "BibTeX" and "Makeindex", and finally click the "OK" button. When clicking "OK", it is expected that the steps you just configured are somehow saved and ready for use. What is actually happening with me is that the steps are just discarded; nothing is actually changed.
Below, I have included a video to show what I am talking about.
My TeXstudio setup:
Version: TeXstudio 2.10.8 (installed from Ubuntu Xenial Xerus repository)
OS: Linux Mint 18 Cinnamon 64-bit
Linux Kernel: 4.4.0-21-generic
It works if you switch to advanced option mode.
Nevertheless it should also work otherwise ...
fixed