My situation is a bit different as I sit at a corner desk. Maybe I'll change it up.
I think that may be where the problem is
I'm guessing if you were facing the corner of the desk (With the keyboard and monitor in-line), that either your elbows would not have freedom to move or your chair would not go close enough in due to armrests being in the way. If the latter is the case you would be leant forwards or your arms would be stretched out slightly, causing stress/strain in one place or another. Or maybe you are square on to the desk as I described, but with the monitor at an angle to the keyboard, which can cause problems too.
A setup like this should be fine (Except for the chair, armrests are too high, need one with adjustable or removable rests):
Whereas a setup like the one below would probably cause you a lot of discomfort. Having the monitor at a different angle to where where you are sat, having the keyboard and mouse at different heights and having to stretch one arm out for the mouse is not good, they should ideally be in line so as to not place any stress on your arms, neck or back.
I'm not really a fan of those keyboard drawers either, they were only necessarily with CRT monitors on small desks. I'm not saying you should get a new desk (If a corner one fits in your room nicely, there is no reason why you shouldn't keep it) just try and arrange everything where it is in line and give your forearms somewhere to rest, but make sure your elbows are free to move a little otherwise this can cause stress in your shoulders/neck and in your forearms.
I've had a desk before that didn't have the depth to accomodate everything, so my old CRT monitor had to go to the side of the keyboard. It was a nightmare ergonomically, putting stress on me whichever way I was sat.