The fact remains that in 2001 a report indicated that there was a problem. You say you believe, in the light of your personal experience, that there was no problem. But there was one. That is what the Transportation Safety Bureau tells us.
Your director of civil aviation tells us that Transport Canada decided not to bother with this issue. That is a choice you made, but the result was that, within the safety management system you set up, people did not take this situation very seriously. In fact, it was not a priority for your department. In theory, the SMS should also cover any problems related to maintaining logbooks, shouldn't it?