This is probably because pre-punching makes small ridges on the bottom of the card, and an identical pattern of small troughs on the top. The ridges tend to get caught in the troughs. Detached chad can become stuck in the feed path, increasing double feeds and misfeeds. Detached chad can jam two cards together, increasing misfeeds. In some machines, detached chad can jam over the light or sensor, causing holes to not be read until the chad blows out of the way.
Detached chad can migrate from one card to the next.
Any damage a card has sustained can confuse a card reader or cause it to malfunction. People are better able to deal with such problems. Cards that have had one or more trips through a high-speed card reader will appear different to a human reader than they would have when freshly punched by the voter. The results of the 2000 election show that it is now time move beyond this temperamental antique. If people voted from home, it would be very difficult, perhaps impossible, to assure that those who vote are who they say they are.