If I use the CKEditor plugin in an HTML page based on a Bootstrap template, it works great, however if I insert the editor on a Bootstrap Modal like this
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Just open /core/config.js in ckeditor files than change "baseFloatZIndex" variable
baseFloatZIndex = 10000
to
baseFloatZIndex = 20000
It will change the start "z-index" of your editor box and the popups.