Okay, got a response from Manila to my email.
Appendix "A" just needs to be filled out, scanned and returned to them by email. They do not need my wife's passport yet.
Appendix "B" (passport photo thing) was sent to us in error. I can ignore it.
Her CBC was unsatisfactory because it did not include "lapsed records". So Korea2Canada nailed it. There was a problem with the search.
I'm a little pissed. I left the gathering of the Korean documents up to my wife, but gave her that sample CBC request form from CIC's website. She tells me that the folks at the police station weren't interested in it, but said that they knew exactly how to provide a search for Canadian Immigration purposes. Hmmmmm. Apparently not. :
My wife has no family in Korea who can do another search for her. So now I have to go to the Korean Embassy in Toronto today and obtain a "proxy" document that will permit a friend of my wife to do the search again on her behalf. I will send that document to her friend in Korea by UPS tomorrow. Her friend will do the search, then have it translated and notarized and sent by UPS to Manilla next week. Total cost of solving this problem will probably be about $250.
The good news is that someone in Manila was at least looking at her file and responded to my email asking for clarification in less than a day. I suppose I can be happy about that.