paragraphs split unevenly

There is a differnce, though, in the two examples. In the split column your first column has both large and small text on the first line, but only small text on the first line of the second column. In the second example both collumns have both large and small text on the first line.

Are you using align to grid?  I suyspect waht you are seeing is the result of using a first baseline setting that is other than a fixed value (i.e. one of the choices related to the phyical size of the type), and the largerr type is pushing the first baseline down in the mixed size columns. 

Using an actual baseline grid and a style that forces alignment to it would probably solve this, or pehaps changing the first baseline option to a fixed value in the text frame options.