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:
http://rawtherapee.com/shared/test_images/amsterdam_moving_boat_1.pef
http://rawtherapee.com/shared/test_images/amsterdam_moving_boat_2.pef
http://rawtherapee.com/shared/test_images/amsterdam_moving_boat_3.pef
http://rawtherapee.com/shared/test_images/london_bridge_moving_1.pef
http://rawtherapee.com/shared/test_images/london_bridge_moving_2.pef
http://rawtherapee.com/shared/test_images/london_bridge_moving_3.pef
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.
Here is what I get from three JPEG images as input (no tonemapping on the results, just the HDR preview at gamma 2.6). Without anti-ghosting this produces a fine HDR image. Boosting the contrast in the auto-masked result reveals that ghosting has actually been successfully removed. See also bug #184.
Ok, it seems there is a serious issue here. We will look into it asap