I recently started playing minecraft again, but when I play for more than a few minutes, it changes the windows theme to windows basic, and the cursor flickers every now and then. If I drag a window around, the movement is very choppy. I'm using a script to allow minecraft to use more ram, so I'm going to start playing it without that, but i'm not sure that's the problem, since doing that hasn't caused any problems before.
You may want to reinstall you graphics drivers and COMPLETELY redo your .minecraft without mods, test and see if it does it again.
I found the issue. i'd forgotten that the button used to maximize minecraft (f11) is the same button I use to have MSI afterburner start recording video. It was a "nice" surprise when I found 5 hour long videos hogging the storage space. probably 600 or 700 GB worth of video XD.
MSI afterburner likes to fuck with my windows theme, and when recording, the mouse occasionally flickers.