Rochey is right in that parallel walls cause standing waves. However, with room dimensions, what you really want to achieve is an even distribution of room modes (particularly in the low end). The problem with a square room is that you are going to have room modes (aka standing waves) pile up around the same frequencies causing big spikes or dips in the response. Just because a room is rectangular doesn't mean you won't have room modes pile up either. There are some calculators floating around the net that you can use to figure all that out based on the dimensions. I think you've made the right choice by picking the rectangular room for your control room. I would suggest putting your desk and monitors along the short wall and treating the side walls with some thick foam to control early reflections. That way the reflections off the back wall will be delayed longer and won't destroy your imaging. Just make sure everything is symmetric around your monitors.
Now, there is a lot of talk about splaying walls and such which can help deal with flutter echo and to a lesser degree with standing waves by introducing some diffusion. However, splaying walls will generally not help distribute room modes very effectively, it just makes them more difficult to predict. I'm also of the opinion that the space you lose by splaying a wall could probably be more effectively used by contstructing diffusors or absorbers to specifically deal with the problematic modes like Rochey suggested.
