UserAgent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.106 Safari/537.36

Example URL:
http://lab.html5test.com/bugs/csscolumns/index.html

Steps to reproduce the problem:
1. Load URL

What is the expected behavior?
The URL contains a div as a wrapper, containing three divs of different heights. The wrapper has the column-count CSS property set to '3'. The children have the -webkit-column-break-after property set to 'always'.

This should be rendered as three columns of different heights

What went wrong?
The second column does not fit vertically, overflowing the the third column. This causes the third column to overflow into a fourth column outside of the container.

Does it occur on multiple sites: Yes

Is it a problem with a plugin? No 

Did this work before? Yes Chrome 50

Does this work in other browsers? Yes 

Chrome version: 51.0.2704.106  Channel: stable
OS Version: OS X 10.11.5
Flash Version: Shockwave Flash 22.0 r0

This seems to be related to the padding-top on the column itself. That padding is not taken into account when calculating the height of the container.

Setting the padding-top to 0, lets the content flow into the proper columns again.