Brand new build (Core i5-7500 3.4GHz Quad-Core, 200R ATX Mid Tower - System Build - PCPartPicker), 2 weeks old, running Windows 10 Pro. No graphics card, connected to my monitor via HDMI. I put it to sleep every night and half the time that I wake it up in the morning, the windows I had open (iTunes, BitTorrent, etc) have been resized (smaller) and moved to the upper left corner ( I have a 21.5 inch Asus monitor, with display scaling set at 125%. I also have a Windows Command Script running that fixes an issue where the text of all my programs was blurry, the contents of the file are:

REG ADD "HKCU\Control Panel\Desktop" /v DpiScalingVer /t REG_DWORD /d 0x00001018 /f
REG ADD "HKCU\Control Panel\Desktop" /v Win8DpiScaling /t REG_DWORD /d 0x00000001 /f
REG ADD "HKCU\Control Panel\Desktop" /v LogPixels /t REG_DWORD /d 0x00000078 /f

I have also went into the registry and made sure that the ActiveSize and PrimSurf values are 1920/1080 and that Stride is 7680. I do not turn off my monitor every night either. Any ideas?