I've noticed that KDE's RandR configuration tool is…oddly behaved at times (even recently when helping a coworker set up 3 monitors). The command line is much better for RandR configuration (I've found no GUI that is faster to get what I want or more convenient) and I have a script in ~/.config/xinit which gets sourced to set up rotation and positioning upon login (no modeline commands though, just relative placement).