System Restore is not “perfect”, to say the least. Sometimes it can mess with installed programs, specially with those that are interacting “deeply” with Windows (like drivers, for example). Having more than one folder (even if you deleted the “additional” folders manually) is such a sign of something messing with your Avast installation.

Whenever you can, follow the instructions so to clean up the (potential) mess, or at least be aware of any potential problems. If you happen to have problems with Avast, start by “cleaning” the potential mess first (removal utility of Avast under Windows Safe Mode). In any case, when you have time for it, it could be useful to report back.