since the hardware that i run my Ubuntu mate on isn't that common, being a 2-in-1 lenovo laptop , i was unable to find anyone with a similar problem to mine. that is the rotation of the screen is sideways as if the system recognizes my laptop as a tablet.
this problem stops after logging in, because i changed the settings of the screen to the appropriate alignment
Open the Displays control panel and tick the box that says Show monitors in panel.
You can now use this monitor applet, the one that look like a monitor with a set square over it below, to flip the orientation of the attached display(s).
I know this topic is old, but for the ones who still wonders for the rotation of the booting and login menu. You can do this : open Displays control panel and once you are done click on Apply system-wide, or aplly for all users. It worked for me.