The "Allow Configuration Word Programming" is when you first program your controller with the HID Bootloader Software you will need to tick that box.
Duo/Raven means you should wire the chip up like in the diagrams for Duo/Raven & Use the Duo/Raven Driver Downloads.
For the difference look...
Re: support center question.
They have to respond to around 50+ Support tickets a day so it takes them a while to get through them. Give it a few more days.
Whatever the preset consists of should not affect when its being programmed.
Try plugging your controller in and erasing it, then unplug and turn it on/off and re connect it and try and load it?