Found that in the latest beta, the CSS classes (gf_left_half, gf_right_half) work fine on a page with no conditional sections below it. As soon as a conditional section is below the fields that have these classes, the layout becomes wrecked (ie. the section appears under the field that has the gf_right_half class).
In my test form (on my local server), I have a conditional section at the top which appears fine. All other conditional sections exhibit the above behaviour. This issue also appears if an element (eg. checkboxes) is put above the section break of the first item.
If any non-conditional elements are above the conditional element and below the elements with the new classes on, everything displays normally.