There are two major problems with electronic voting. (a) It's often not implemented very well (either due to malice or incompetence; probably a bit of both in some cases). (b) When something goes wrong, and it will, there's often no reliable way to figure out what or to fix it.

With sufficient effort, a 100% reliable paper count can be produced. Of course in many cases it may not get that effort, but it's possible, and this attribute is particularly important in an audit.