Update CkHelper.php
Update CkHelper.php

defaultOptions did overwrite custom options.

http://php.net/manual/en/function.array-merge.php
If the input arrays have the same string keys, *then the later value for that key will overwrite the previous one*. If, however, the arrays contain numeric keys, the later value will not overwrite the original value, but will be appended.
MichaelHoughton/CkEditor