From eefje234... "Reason was hidden text. There were a few pages that had a layer that was placed outside the regular screensizes (it was done years ago). For most of the pages this was removed long ago but some pages were forgotten."
I believe this is a very common situation. After all, many of us have reached the 10 year anniversary of being on the web, so inevitably there are going to be old pages that have not been modified in a long time because the info is still useful. And yes it is conceded that someone may have done something incorrect to those pages at some point along the way. For those of us who remember the late 90's, many theories of getting fully indexed were floating around.
What I do not understand is why Google feels it is necessary to penalize an entire site -- why not simply remove all the offending pages, and leave the rest alone?
It is like throwing an entire team out of a game because one of the individual players purposely bumps the umpire. The officials throw that player out and then the game continues.
Given how important Google is to the economic success of a small business -- and thus the livelihood of their employees -- such a brutal punishment is downright cruel. That is not the "good energy Google philosophy" that they've spent so much time cultivating via their PR department.
The public sees one Google but the webmasters too often these days see another, and that's too bad because it's unnecessary.