I haven't had time to review the entire thread so excuse me if I cover old ground.
I experienced the same problem this week where CuteEditor would log me out in a child portal environment.
Basically, I copied a live working installation locally and updated my portal aliases accordingly. I then found that when I logged in as a standard user and visited a page that hosted the CuteEditor, I would be logged out on the next post back.
I managed to fix the problem as follows, however, this might not work for everyone as my application only uses the text editor in a specific portal - namely portal id 5.
In IIS I had set up a virtual directory for my installation using an appropriate name (e.g. localhost/website). This means that the portal aliases table had to be updated to enable me to work locally, i.e. localhost/website/portal1, localhost/website/portal2, localhost/website/portal3, etc. I also created an entry localhost/website so that this would be picked up by default when I ran my application in Visual Studio. Unfortunately, I had assigned this last entry to portal 3 – not 5 where I use the text editor control.
By changing this last assignment to portal 5 I was able to fix the issue. This will not work for installations where the text editor is used on multiple portals but hopefully this should point people in the right direction.