What you describe is 100% correct ! At the time you change the Dreambox channels list then you also need to update the channels list for the web control. The Enigma-TV tool do not check your Dreambox settings automatically, you have to be aware on your changes. You did it right !
Have not used the program for a while and upon opening it said that a new update was available downloaded this and it had saved my details which is of the updates. I could view locally but as soon as I tried to use via the Internet it would crash the program and the Dreambox, I eventually solved the issue by updating the web set up file within the program, it appears if this is significantly out of date it will not match the indexes on the box causing both the program and the box to crash. I will regularly update this file as it is quite vital to the running of the program