I installed 16.04 and upgraded to 16.10 and experienced this on both versions. The default programs' windows don't remember their location. For example, when I open the file explorer or the terminal, the windows both open with different sizes and locations all the way on the right bottom of my screen. I can then center them and resize them, but when I close them and reopen them they are back to the way they started (bottom right of my screen and the wrong size).
If I install a program myself, however, the program's windows remember their location and size.
Why is this happening?