I agree that it is strange that CI would not issue an boarding pass to you in transit for their own flight, my only guess is that maybe they were not able to do document check at the transit desk and that, they usually have document check done at the origin airport to allow for printing of transit boarding passes at TPE and couldn't rely on the document check performed by the low cost carrier because their computer systems don't talk. It's also possible that this is a punishment for not using a partner airline for the original leg and trying to get people to not travel on separate tickets.
FYI: Since this isn't about EVA air specifically it will likely get moved to the Other Asia Forum in Destinations.