Folders that I have listed in "Do not scan these folders:" in the configuration show up in my scan. Reproducible: Always I'm pretty sure this used to work. I can't tell you what version as I haven't run it in a while.
Actually I just discovered the problem. All the folders listed in my Do not scan list ended with a /. E.g. /home/ericjs/stuff/. I tried deleting and re-adding a folder, and it was added without a terminating /, like "/home/ericjs/stuff". Rescanning resulted in this directory properly being ignored. I'm pretty sure these folders had a terminating / because that is how a previous version of Filelight created them (I certainly wouldn't have added such a slash myself). So this would seem to be a backwards compatibility issue.
fixed by joachim in b06ec65e0c79d8eea8e44d4367364fd572c3dd19