Hi Matthias,
I wasn't able to reproduce exactly what you describe, or at least not how I understood your description. By adding another Button on the left panel, that would only add to the CKEditor.Text and do nothing else, then no matter I used F5 or not, the Text of CKEditor always got updated, so as far as my tests show, the server-side is indeed "connected" to the correct CKEditor instance on the client.
I did however notice what might be the problem you are describing. Because of how the client layouting engine works, and the fact how your controls are constructed, with UserControl docked to top, UserControl docked to bottom and your CKEditor docked to fill, then when you change your "toolbar" like UserControl subcontrols, it will have a triggering effect on the client layouting mechanism, which will result in a reload of CKEditor. The CKEditor client resources are huge, and relatively slow to completely finish loading and initializing, and while they are loading + initializing, there is a small window where invocation of client methods will simply get lost.
I consulted with the lead developer in trying to find a way to prevent CKEditor from loading in this case, but we did not find a way to prevent that on the current version of the framework. I therefore implemented an optional delay that you can place on the commands issued to the client-side of the CKEditor control and you can find the most recent version (v004) uploaded on the CKEditor article here.
This new property is CKEditor.CKInvocationDelay and the value is in milliseconds. You can set this via the Designer, or you can set it runtime. Using your application, then within the CreateEditor() method, I set ckEditor1.CKInvocationDelay = 500 which seems to do the trick.
I tested this in the most recent version of the framework, both WinWeb and .NETHTML5 and as far as I could see, there wasn't any problem.
Please try this new version of CKEditor and see if it fixes your problem.
Palli