In the assets tab, I have created a group to which I sorted all my "good" and "bad" movies after movie alignment into few groups. When I tried to pick this group to use in the next step (CTF estimate) no groups are available, only All movies option is present. If I run the CTF estimate on all my movies, in the results of this run, I can't assign any of the movies to a group (the option is greyed out)
Any idea what would cause that?
The CTF estimation input is a group of images (even if you run on movies). So you need to create a group of images. You can create a group of images which corresponds to your group of movies by going to Assets->Images->New from movie group (this is a button on the bottom left, under the groups box).
Does that solve the problem?