Sorry, I should probably put more info as to what I have done.
The screen is on the DSI-2 port, res is 1280x800 at 40Hz, so I used "video=DSI-2:1280x800M@40,rotate270". This didn't work for me either.
In the config.txt file I have also tried lcd_rotate=3, but also didn't work
Everything on my display is the correct orientation (boot splash screen, terminals, desktop etc.) except the kiosk screen. I think it is more to do with the dtoverlay driver that Edatec is using for the screen as they have a custom interface board between the pi and LCD.