I think you've tracked it down. Windows, differing walls, and doors are all possible influences. A few things I saw from the pictures: since the bookshelves are open on the sides (not a bookcase) and sparsely spaced they aren't really going to be greatly affecting the bass. The filing cabinet against the wall may have, but you've removed that. Also, the size and configuration of the panels over the windows maintains the windows as a factor for your bass issue. So yes, less than a revolutionary post here, I know, but my vote says you've got a working idea of the problem. The good news is that problems like this, if minor, can sometimes be pretty benign in your everyday work. You may not notice it in context (I believe you've said as much) and your ability to work may not be significantly impaired. Good luck and good listening!