I agree that it is anomalous. My original UCI was given to me on a VR (I came up to Canada as a "Seasonal Resident" and that meant issuing a VR.) It was in the same passport that I used to obtain my work permit (original UCI) as well as the FSW application. It seems to be Sydney, Buffalo or NYC (the three offices that touched my FSW application) that created a second UCI. *I* didn't notice it until I was going through the CAIPS notes for my FSW application last month. Of course, since that's now off in Federal Court (application for judicial review was filed last Wednesday) CIC doesn't want to hear ANYTHING from me about that case. I'm starting a second (spousal sponsored) application now and I'm using my original UCI.
I wish I HAD known the FSW was done under a different UCI - it would have lowered my stress level about crossing back and forth over the border (since now technically, even with a valid work permit they could stop me, cancel the work permit, and send me back to the US because of the FSW finding of medical inadmissibility.) Having it listed under a different UCI means the likelihood of them matching up the FSW rejection with the work permit would have been even less likely. Every time I cross, though, I'm grateful for having Nexus, because I don't have to speak with an IO at the POE (when flying) and the scrutiny level is lower even at land border crossings.
It will be interesting to see which UCI they use for my new sponsored application.