I'm observing the same issue seen in QGIS map composer changing legend position when exporting atlas as images It is happening when the checkbox "Main properties > Resize to fit contents" is checked.
Also I can observe that the
Y position on page
n is what should have been set as
Y position calculated for page
For example is the legend was tall on page 2, and short on page 3 then it is floating high on page 3 instead of being anchored at the bottom of the page where I want it.
The upvoted answer in QGIS map composer changing legend position when exporting atlas as images won't fix the issue in my case. The only way that I found is unchecking "Resize to fit contents", which is not satisfactory for me.
Page 1, tall legend:
Page 2, short legend:
Page 3, tall legend:
I'm using QGIS 2.18.24 on OS X El Capitan.
I have the Legend properly anchored, here is the preview of page 2: