[java]- trying to change baseDir/baseURL for each user

http://docs.cksource.com/CKFinder_2.x/D ... /Extendinghttp://docs.cksource.com/CKFinder_2.x/Developers_Guide

Since configuration is loaded in init method it seems like a good idea but it would meant modifying CKFinder core files and we don't consider as a good practice.

A much better approach would be to extend ConnectorServlet. All methods in new servlet would only call super.methodName(…) and init method would additionally have something similar to this line getServletContext().setAttribute("ConfigurationKeyName", configurationField);
Of course changes in web.xml are also required in this case.

At first glance it looks like something was not reloaded and that is why CKEditor is using old paths. When user logs out and new one logs in, one might expect that whole configuration gets cleared away and the new one gets loaded. Looks like you have a security issue in your app.

What addresses for requests do you see in Firebug?

This might have something to do with my previous post. I have told you that you can place your configuration in the scope of application - it means that configuration object will be in server memory as long as the application runs thus it will be the same for every session. This method is good for resources that can be used by every user of your application, are not changed very often or/and loading them into memory might take some time.
If you want to use new configuration object for every user (READ EVERY SESSION) you should place such configuration object in session scope for every user (and of course invalidate session when user logs out).