Another option would be to preprocess the DocBook DTD using James Clark's SP tools, which could strip the comments for you and reduce the size of the DTD used during processing.
This part seems directed at me, since I'm the one dealing with DocBook.
This is not a bad idea, but doesn't really solve the problem, which is that these comments are appearing in my documents in place of the DOCTYPE declaration that should be there. Granted, maybe I'm not familiar enough with the formal XML specs, but this certainly doesn't seem a valid transformation for the round-trip through Xindice to be making (though, again, it seems like Xerces' fault). Even if I could strip out or ignore all of the comments, I still wouldn't be getting back the same document.
Sixten
