I think it's an exif issue. Can you try if this helps?
- convert the CR2 to DNG with Adobe DNG (lossless)
- process the DNG with cr2hdr
I always set WB manually, so I can say I don't have this problem

If it's daylight, it's easy (something around 5500 in sunlight, 6500 in shadow). A little magenta boost when shooting grass with older lenses. Indoors, I found balancing on something white a bit too harsh (I prefer to go a little warmer from there). Sometimes I get much better results if I do the white balance directly on skintones.
I have a small modification to ufraw that lets me do spot WB on skintones; if anyone is interested I can share it.