Since AIJ is creating a new directory for the aligned images, I think you opened the images as a "virtual stack". If that is the case, can you try opening the images directly into memory to see if you still have that problem? In this case, the images will be keep in memory and not written to a subdirectory. Let me know if you still see the problem.
One thing to check. Make sure the option "Remove background and scale to common level" is not enabled on the alignment setup panel.
Either way, if you can send me the two sample images directly to karenacollins at outlook dot com, I can try to reproduce the problem on my system. My limitation is that I run Microsoft Windows and don't have access to an Ubuntu machine, but if I can't duplicate under Windows, I can try it on a system with an alternate linux distribution.
Karen
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