The multi-column list guide suggests wrapping the list in a div with a style attribute, but doing so generates CSS that is not entirely correct. The top alignment of the first item in the first column is not the same as the first item in the other columns, and the result is that the first column will sometimes be 1 element shorter than the rest. This can be observed in this example of div col in Chrome and Firefox by resizing the window so that the list is arranged in 5 columns. In Wikipedia, the div col template circumvents this by overriding the default style, resetting the top margin to zero in the wrapped list element (ul, ol), which is defined as a non-zero value by the class mw-content-ltr.
I believe the solution is to add the div-col class to MediaWiki's CSS using the same trick as in Wikipedia.