Since IBM released FP2 I dabbled around in my apps that use the CKEditor they just updated to 4.3.2 (against 3.x something). I understand that IE11 support had to come but this fixpack is really pain in the ass if you deal with CKEditor and custom skins - and the type of toolbar you want to present to the user.
What I learned so far: you can EITHER
BOTH use the Dojo attribute "toolbarType" (FP1 and prior) or and "toolbar" to define the toolbar functions ("Slim", "Medium", "Large", "Full") without having trouble either on FP1 or FP2. You may use BOTH if you installed FP2 and reverted to FP1 again due to the problems FP2 makes since the Dojo recources for the CKEditor seem to be not be removed by the uninstaller. I have to say that this fixpack is the plain chaos and I really advise you NOT to use it.
What causes problems in my case is the usage of a custom skin, esp. the Bootstrap skin. For FP1 you can use this one - but this won't work with FP2. Instead you have to use this one - but it won't work with FP1 *ARRRGH*
If you compute your server's release regarding the fixpack installed then you may come around. I have to admit that this is way too much for compatibility reasons to do so I decided to leave the skin alone and present my CKEditors in the default style - sorry!
I just released a new version of my FileSilo on OpenNTF. This release 2.0.3 doesn't use the skin anymore and has been designed to work in both environments.