Sorry I never responded!
I haven't posted on the Phase One site about this issue yet. I did some searches in their knowledge base and found this article:http://www.phaseone.com/Search/Article.aspx?articleid=1168&languageid=1
I tried the suggested steps and it unfortunately did not fix my problem. However, in the course of playing around with the problematic files I noticed that they did not seem to have an embedded color profile at all. I opened some up in Photoshop and assigned a color profile (after discussing it with a friend in publishing I selected EUROSCALE COATED v2), saved and closed.
The new thumbnails in EM after a rebuild look good! I tried other CMYK profiles in Photoshop, but this seemed to look the best in EM. I searched EM for all CMYK images with no color profile, opened in Photoshop, and ran a custom Action to assign the color profile, save, close.
It doesn't totally solve my problem as I still have wonky looking CMYK jpegs (I don't want to do a lossy save after assigning a color profile, and I haven't found a way to assign a color profile without having to re-save the file after to make it stick.) But my tiffs look good, so that's a positive step!