Upgraded drivers for one. Sam Tellig reviewed the 1.3SE's several years ago and discussed the differences - it might be out on the S'phile site. He characterized the 1.3SE as Dynaudio taking the 1.3 and reworking it without working to a specific price point.
I heard the 1.3SE in a nice dealer setup once - the difference between a good amp and an excellent amp was readily apparent, and the sound was excellent. I've never heard the 1.3 so I can't comment on comparing the two.