Take Expatriates.SE.
The site you link says 96% of questions are answered.
There are 379 non-closed questions. There are 357 answered questions. 357/379 = 94.2%
If we remove the switch for closed, we get 423 questions and 384 answered questions for a percentage of 90.8%
If we only look at accepted answers to non-closed questions then we get the same 379 questions, and only 176 answered questions which is 46.4% answered.
So I think it's clear that the conditions are something like:
Non-closed questions with > 0 answers
-------------------------------------
Non-closed questions
The difference between the 96% shown on the site list and the 94% through advanced search could be caused by (pick 2, they're small):
- Caching
- Unicorns
- Deleted Answers
- Deleted Questions
- Y2k bug
- One of the Tim's
- All of the above