I have noticed this problem for a long time; this was one reason I have always thought replacing embedded PDF viewer in TeXStudio by Sumatra PDF. But I think this problem is related to compatibility issues of TeXStudio Embedded PDF viewer with Windows 8/10 64 bits OS or the screen resolution of your computer (16:9 screens are more problematic). In my home I have a desktop computer with 4:5 screen and Windows 7 64 bits and a new laptop with Windows 10 64 bits. TeXStudio with his Embedded PDF viewer is working perfectly in my Win 7 desktop PC, but I have the problem of forgetting "maximized window" by the embedded PDF viewer in my Win 10 Laptop. I managed to get around a solution: the first time you launch the embedded viewer try to maximalise his windows "manually", i.e. by dragging it to the center of the screen, then mouse-dragging the corners of the viewer window to the top right & left corners of your screen. When you are happy with result, close the PDF viewer. The next time you compile a tex file in TeXStudio, the embedded PDF viewer will remember his "maximized window". So the PDF viewer dont save window settings if you use "maximize button" at the top left corner but save them if you do it manually by dragging the corners. Alternatively you can edit the settings:
of the file C:\Users\UserName\AppData\TeXStudio\texstudio.ini
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