I think the reason 4 units would get split as 2 per box is that's actually cheaper shipping than packing 3 and 1, since 3 DVDs would total 15 oz. fully packed and thus be ineligible for First Class. E.g., following your scenario above and looking up rates manually at USPS.com:
For 4 units:
+4.95 (3 DVDs @ 15 oz. Priority)
+2.24 (1 DVD @ 7 oz. First Class)
=7.19
vs.
+2.92 (2 DVDs @ 11 oz. First Class)
+2.92 (2 DVDs @ 11 oz. First Class)
=5.84
Adding $2 handling and 2 boxes priced at $0.50 each, the latter should come to $8.84, which is exactly what the cart calculated when I tested it.
However, for 5 units:
+4.95 (3 DVDs @ 15 oz. Priority)
+2.92 (2 DVDs @ 11 oz. First Class)
=7.87
Adding $2 handling and $1 for 2 boxes, this should come to $10.87, but the cart calculates $9.52, a shortage of $1.30 that I can't account for, so I'll have to ask Development to look into what might be going on there.