Why are “new” flags of mbox folders wrong in folder-list view?
As written in manual.txt, the flags are determined by comparing the timestamps of last access and modification. This can get messed up if the folders are “touched” by other programs than mutt, like “biff” or backup software. There is also some issue with the “noatime” flag for mounting filesystems (most often used on laptops). If “noatime” is activated, no timestamp is updated for the last folder access, i.e. Mutt cannot determine if the folder has received new mail since last visited. For mutt before version 1.5.15, you can recompile it with the –enable-buffy-size option to “configure”; for mutt 1.5.15 or later see the $check_mbox_size option. Mutt will then use the folder size instead of the access times. (This is only a workaround and might give suboptimal results; another option is to use the MaildirFormat.