Inaccurate Audio Preview

Since they removed multi threading AE really took a nose dive in playing back audio in real time.  To compensate they made it so it preloads a second or two of audio which gives the illusion that they fixed the problem.  Problem is, as you've discovered, you can no longer use the waveform as a reference point.  I've gotten used to it.    You just have to learn to live with it.  As Mylenium said, it sucks but its just the way it is.  With practice you'll just get better at recognizing the waveform patterns within that short offset. 

You may also notice audio drops frames all the time which, when dealing with narration, could make plurals sound like singulars or drop out articles like "as" or "the".   It makes difficult to tell if the narrator made an error or the audio is dropping.  In those cases I I have to shorten the playback duration to 5 or 6 second and let it loop through once.  The second time through it will play the audio correctly.   But if you stop and restart without letting it loop through it will always drop the same frames.   

It might make more sense to prep such stuff in Premiere/ Audition and import the edits and markers from there. Not saying that it doesn't suck, but AE never has been good at exact audio timing as far as I can rember for the last 25 or so years due to it not working sample-exact. Current issues in AE and the underlying OSs clearly don't help as you already found out yourself. Sorry I can't offer a more optimistic and positive answer.

Mylenium