I am currently trying to render a 2048x1024 Map (or rather 3...Normal, AO and Diffuse) using 3ds Max (MRay) and it seems to me that it is of lower quality than it has any right to be...apparently Max renders it full 2k and resizes it afterwards...when I watch the Framebuffer during rendering, I can see details nice and crisp that are completely blurred once the Map is on the model, both in Realtime Display and Offline Rendering (also MRay)...is Max' resizing algorithm that bad and I should be rendering full 2k and resize using PS or is that just my imagination?
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For the render, try turning off any sampling on the texture and re-render, I find with Mental Ray the default texture sampling makes a lot of textures look much blurrier than they are. You should be able to do that in the Bitmap's properties in the Material Editor.
I don't recall ever having issues baking non-square textures in Max, so I'd recommend trying those things out first.
I did a few non squares recently with the scanline with no problems. why are you using MR? Scanline tends to be much better for baking as you get the gloabl super sampler