A380: Repeating the 747's history?

I'm somewhat surprised to see Airbus having such difficulties
considering the A380's having been designed on a computer (3D digital
mock up). I thought the main benefit of CAD was to have the ability to
test for systems integration before any metal is cut(?) Of course this
is an extremely complex aircraft with many complicated systems that
must all play together, and the latest wiring harness issue may not be
related to any design deficiency.
By comparison, I recall seeing a documentary on the 747's service entry
(1970) that had its share of gremlins. (IIRC a big source of headaches
were the Pratt JT9D fans) The documentary didn't go into much detail
about the program's problems, (I'm sure there were a few) but that
airplane was designed by engineers on drafting tables and not
computers. I just assumed new aircraft designs would have smoother &
shorter development because of modern computing power.