Scan is disabled (or just straight-up broken) on this version because I couldn't test it. I got greedy while testing the one Dye Amp I had that returned a great result, and lost it forever.
Auto Position should align itself to be on top of Vindictus' Dye Ampuole screen, which won't be centered. I also forgot to mention that Auto Position requires Vindictus to be running at native resolution, and fullscreen.
Hopefully this helps! If it still doesn't work, please provide more details/screenshots/anything.