The bookmarked entries on my Nautilus Sidebar change positions in the Sidebar stack. I most frequently see them move after removing a USB thumb drive after having done some work.

Say my Sidebar looks like this:
1-Desktop
2-Papers
3-Projects
4-Records

I will insert a USB thumb drive, do some work and then when I eject the thumb drive and remove it from the computer I often see the bookmarks move. So they now might look like this:

1-Desktop
3-Projects
4-Records
2-Papers

I do not understand what causes this movement but it seems to most often coincide with USB thumb drive use.