This puppy as you might have noticed is actually physically 2 separated devices in one box:
There is a zwave relay with its own chip and a scene controller with its own zwave chip.
Coming from factory, the button 1 of the scene controller is associated to the local load relay. The 2 are actually wirelessly connected through zwave.
When you paired it to the vera, the vera sees the first device like any other leviton 4 scene/zone controller and wipes out all the associations.
In order to make the first button (or any other button for that matter) control the local relay, you will have to associate them manually.
How???
Go to your scene controller device and go to the device option section.
Here you can define new user associations.
Type "1" in the group id field and click add. Now you can define which device will be associated to the button!
Under "group 1", click set and you should see a list of all your zwave devices. Check the local load.
Note: You will have to have the vera very close to the leviton since the vera will have to configure the controller...
You can go on and associate any other devices to groups 2, 3 and 4. Each corresponding to the buttons on the scene controller from top to bottom. You may have to repeat the association several times as in my experience, the setting from the vera sometimes gets lost.
I have all my leviton controllers set up in direct associations whenever I can. They will send the zwave signals directly to the device instead of going through the vera and therefore can work without the vera. There is also much lower lag of course. You can even directly associate multiple devices to a button. Direct association is also the only way you will make the dimmer (last button at the bottom) function on the scene controller work so you can dim all kinds of dimmers associated to the button.
Hope this helps.