Bug 40325 is highly related to this but it is NOT fixed in 5.4.0.3, at least not on Mac. Looks like it was an OO.o problem originally. Trying to print slides in Handouts mode. The two "Order" selections are "Left to right, then down" and "Top to bottom, then right." Either selection results in "Top to bottom, then right" rendering, at least when saving as PDF from the Print dialog (have not tested with printer). There is a workaround posted in 40325 - explicitly set slides per page to 6 - but on the Mac at least I can't find a place to do that; the online docs refer to tabs that don't exist in the Print dialog and there's nothing about that that I can see in the Properties under the Handout Master view. Still, the selection in the Print dialog when Handouts is selected should have an effect and currently it does not.
CORRECTION: There is indeed a "Slides Per Page" drop-down in the Print dialog and changing it from "According to layout" to "6" did make it work correctly. Still, the setting should have an effect on the handout slide print order.
Can confirm, same issue as bug 99301 *** This bug has been marked as a duplicate of bug 99301 ***