It simply just didn't download them again but continued with the ones that hadn't been loaded yet
By adding the individual files to the download list, they get added to the duplicate detector. When you add a complete set, the dup data doesn't get added till after the complete set has downloaded. Sounds to me like you were depending on a bug which has since been fixed.
I'd say if you download 2 rars from the set, then decide you want it, use Ctrl-Y to add the main set without the dup detector. You've already decided you wanted it at that point. Ctrl-Y won't re-download the two you already downloaded in the latest version.