Awful canon raw conversion for photos with dramatic (i.e. underwater) non-standard white balance

I'm shooting underwater (and white balancing as I shoot using a white disc) with a canon s90, and have noticed that the raw conversions done by aperture are way worse than those from jpegs when I shoot in raw+jpeg and those done by raw processing using the canon digital photo professional software. In particular, reds are pretty much lost. It may be a false lead, but I notice that in aperture, the rgb histogram shows a dramatic spike of the red channel on the far right (possibly clipping?) that doesn't show up in the rgb histogram in the canon software.

I'm not sure whether this is related to the plethora of threads about canon raw processing and overly green output. Has anyone else experienced this or have any ideas? I could batch convert to tiff in the canon software but I'd really rather not do that... For one thing the 16bit tiff files are so much bigger than the raws and it is an annoying extra step. Also, note that I can't just batch fix the white balance because (a) I'm having a hard time getting aperture to do it properly (possibly b/c the red channel is clipped as far as the aperture UI is concerned?) and (b) The white-balance changes from picture to picture as I change depth, which is the whole reason I white-balance as I'm shooting in the first place..

I've attached two versions of a picture, one of which I processed the raw in aperture and one of which I processed the raw (and converted to TIFF to give to aperture) in the canon software. I then exported both as small jpegs from aperture.

Canon Digital Photo Professional (correct):

Aperture RAW processing (very wrong):