no, I was wrong. Reconstructions are still fine, however I noticed that if I replace a photoset (delete the directory and replace it with new photos) RC messes up. Aligns and recontructs the previous set, even after closing the application.
It maybe even makes a merge of old and new sets of photos, which leads to the “useless” reconstruction which I was talking in my previous comment.
Using a new folder name for a new photoset removes the problem.