I couldn't get this tool to work well, ever. Ghosts are not removed, non-moving areas are messed up, and image hue is changed (the latter especially when using TIFF images instead of raw).
Please give these images a try:
From TIFF files: http://i.imgur.com/b9PO0NZ.png
From PEF files: http://i.imgur.com/gFfQCTw.png
I used align_image_stack, auto-crop and auto anti-ghost. align_image_stack is not to blame as it does align them well. The TIFF images I used are fine, they are just sharpened and demosaiced properly, no curves or any exposure tweaks, they make great HDRs when not using Auto Anti-Ghost.