Here I go, answering my own post...
This thread, still unanswered from June of 2013, explained my problem: http://communities.bentley.com/products/road___site_design/f/5922/t/87467
The XIN in question had a corrupt FeatureCategoryCollection, where most of the features from the FeatureStyleCollection were missing. Apparently, I had created an XML Report that would create a new FeatureCategoryCollection that can be copied and pasted into a faulty XIN file and it fixes the issue. Interestingly, in the past, I only noticed issues from my linked survey xin. This time, the Survey XIN seemed to link OK, but the Cicil Preference would not.
I have always advocated that there should be a master XIN file used by everyone following a standard and if you can't work out the trading off of read-write access, then a copy was permitted, as long as any enhancements developed in the copy were evaluated for potential inclusion into the master. The idea of separate survey xin and design xin files begs to end up with DTM feature styles that the desin XIN does not contain. The only reason for two is so that the default preferences can be set to existing or proposed, but in reality,since the default preference is now in project defaults, even that argument falls flat.