Hi Paloma,
We are using the auto attendance module too and our staff is not really convinced in using it because we're getting some odd errors from time to time and there's no documentation out there but there are some people willing to help so.. : )
Just before hitting save I was getting an error about a missing ID and I found out that this problem occurs when I'm trying to take attendance of students in a course where I had a lot of users enrolled coming from different groups. When I deleted some of the enrolled groups to minimise their number it worked. Haven't found a way to solve this issue but at least I know I can't use the module across all the courses unfortunately.
I don't know if that helps at all but I hope it does or at least it gives some useful feedback to the developers.