I've noticed some of this lately, although the differences in my routes aren't as drastic, more on the 4-6 minute level.
The thing is, Waze can't predict the future. I don't even think it uses an algorithm that predicts heavy traffic patterns based on time of day. So when you start a 45 minute trip, it is going to show you the quickest route at that exact moment. That may change in 20 minutes. Or even 5.
My frustration is that it doesn't automatically redirect often enough. Just this morning, I was about a third of the way in a 40 minute trip. I was skeptical about the way it was taking me, so I hit the routes button, and saw another way that was 5 minutes quicker. Maybe it only reroutes you if the difference is high enough.