I was testing your ckeditor and I noticed that the link feature does not work.
Repro step:
- show editor in popup (jqxWindow)
- enter text
- make a selection
- click on link icon
- enter something in url and click ok
Result: the selected text is now blue and underlined (like a link) but if you check the CKEDITOR.instances.pageTextEditor.getData() the data doesn't have the a tag html. Also if you click on the source button, the a tag is not there.
What can be the problem?
CKEditor 4.3 (revision d2184ac)

Nevermind I found the problem
Nevermind I found the problem. There was a filter applied to a tags.
CKEDITOR.on('instanceReady', function (ev) { var editor = ev.editor; var dataProcessor = editor.dataProcessor; var htmlFilter = dataProcessor && dataProcessor.htmlFilter; function spanToUpperCase(element) { if (element.attributes[ 'style' ] == 'text-transform:uppercase') { var valueText = element.children[ 0 ]; valueText && ( valueText.value = valueText.value.toUpperCase() || '' ); delete element.name; } } function removeATagWithName(element) { if (element.attributes[ 'name' ] != '') { delete element.name; } } editor.dataProcessor.dataFilter.addRules({ elements: { span: spanToUpperCase, a: removeATagWithName } }); editor.dataProcessor.htmlFilter.addRules({ elements: { span: spanToUpperCase, a: removeATagWithName } }); });