I wrote this article, because I've seen this specific topic many times on many different forums. The never ending talk about seat harness vs. waist harness regarding back pain. But I think it's better to help the back pain first of all, instead of just treading the symptoms.
If you're lucky, you can make the lower back pain go away with a different harness, but only if you're lucky. A seat harness is better, because it doesn't put pressure on your back in the same degree.
I've been working with back pain rehab for many years and noticed something specific about kiteboarders and lower back pain...
From my experience it's very typical for people with a lower crossed syndrome (kyphosis lordosis) to get back pain from kiteboarding with a waist harness. This is because we (I have the same problem!) walk around with too much arch in the lower back all day. If you're lucky, it doesn't cause you any pain in your daily life (yet). But wearing a waist harness increases the arch in your back which is causing the pain.
You can fairly easy check, if you're one of those kiteboarders with a lower crossed syndrome. Check this link out: Lower crossed syndrome (kyphosis lordosis) is the one to the right...
You can do exercises for this, that will help you. It wont take a way the pain, but minimize it. I have a very bad case of lower crossed syndrome and I can wear a waist harness just fine. It hurts a bit, but not that much. The important thing is to have a really strong biceps femoris, gluteus, abs and of course the core muscles.
These muscles work opposite of the lower crossed syndrome and will help you a lot in your daily life and when kiteboarding. If you have lower crossed syndrome, that is... ;)
The other likely possibility is poor flexibility around your hip
This causes pain because the decreased ROM (range of motion) of the hip is compensated by extra movements in your lower back. And this will make your lower back work too much and cause tension. Especially in your lower back in a diffuse area around the lower spine (not directly the spine). This would be quadratus lumborum muscles. This can also be helped with mobility training (I haven't shoot videos to make a dynamic mobility training program yet :( ) or stretching.
www.KiteboardingExercises.com - Power 2 Progress