I haven't been able to isolate any specific situation in which this happens, but every so often Calibre stops grabbing books I put in the autoadd folder.
I've already checked that a) the folder is set to the correct one, b) I actually put the files in the right folder (yes sometimes I've forgotten), and c) the files are of a format that Calibre accepts. I've also checked for read-only flags or file locks but didn't notice any.
It always starts working again after restarting Calibre, but I'm wondering if anyone knows why this happens and how to prevent it in the first place.