Window/wall cutout adjusting help needed

Hi, I'm practising with different winows and there is a slight problem. When I tried to make wide window (referenced snowy escape door so it looks pretty identical even though I made it myself) window is sinking in wall or partially sinking in wall depending on where I place the window(screenshot below). I have a right sized cutout since I basically copied the values from the  snowy escape door. So what could be a problem?

Oh, also! I can't for some reason make a middle lod without some random clipping on one side. Have tried pretty much everything. 

Package

screenshot 1 (fully sunk in wall)

screenshot 2 (partially sunk)

clipping issue screenshot