Even though it seems that the game gets harder when it speeds up, it actually makes it easier to see the notes. It's the best way to deal with parts with too many notes. But, I agree with you, the first time that it accelerates I was just thinking: "Hey, what just happened there?" :-)
I don't know if it has anything to do with song section or not. I have been playing Rocksmith since release and two weeks ago I bought Just Got to Be by The Black Keys. I played the song once and it was fine. Went to rift repeater for one section and played it about 14 times then all of a sudden it sped up big time. (When I didn't pass the section for the record.) All of a sudden instead of seeing like 14 notes on my screen I'd only see like 6 as it was zoomed in or something. When I went and played the full song the whole song was really quick and hard to see any notes. The song is pretty easy, but I'm essentially playing it from memory because it is moving so darn fast...
The best way to explain the issue is this:
Instead of seeing about 4 seconds worth of notes on your screen you start seeing like 3/4 of a second on your whole screen. It's just weird and basically impossible to use.