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It appears that the latest WYSIWYG module release (both stable and dev version) has a bug (or two to be precise) related to CKEditor. I've just tried this on a customers website, as well as on a local, default drupal installation with no other module installed other that the wysiwyg module. The bugs are independent of the CKEditor version used (tried the latest 3.5, as well as older releases such as 3.4.3 and 3.4.2).
The bugs are as follows:
- The formatting icons (bold, italic etc.) are not marked as active when used on a piece of text, hence you cannot remove the formatting once set
- The elements path at the bottom of the editor is missing
Downgrading to 6.x-2.1 solves the issues. I've attached a screenshot with an example.