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I hate answering my own posts but...
OK, even after I posted, I kept looking through older posts and Googling and I think I've answered this one myself. At some point the Cleaning with HTML Tidy option got turned off. HTML Tidy was cleaning these up before but they started appearing once I inadvertently turned this feature off. Once I realized what was going on and turned this feature back on and resaved one of my epubs all the cdata references disappeared.
I thought I'd post what I found out in case anyone else ever runs into a similar situation.
- Byron
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