I'm also loosing my nerves over Kate.
No matter what I try, I can't make it to remember the window layout,and few other configuration options are not saved also. I've tried many desparate things, many editors, but nothing realy beats Kate.
I've tried to start it under root, and I even created new user to see if that will work. Nothing helped, but I'm a bit lazy to downgrade.
I'll just keep kate open 'till end of time
When I don't need it I send it to other desktop
But seriously, if anyone has a solution for this, I would realy appriciate it.
Erol