Lincoln
Like you I find this very annoying .
For me "extracting audio" sometimes results in the audio becomming out of sync with the video, also doing the "update" mentioned above does not fix it for me; I must be doing something wrong?
Having opened iMovie 6 to try "update " fix and failed I started to try a few things.I think I have found a solution that works.
The following sounds complicated, but is not; reading twice is recommended
Most of us apply a string of transitions from left to right i.e. between clip 1 and 2 then between 2 and 3 then 3 and 4 and so on. The audio glitch will occur in say transition 2/3 because there is a transition immediately before it in 1/2 and likewise a glitch in 3/4 because of the transition immediately before in 2/3 .
I find you do not get a transition audio glitch between 2 clips if there is no transition immediately before.
So the simple solution is having sorted all your clips and edited, apply the transitions in reverse direction i.e. from the end of the movie working towards the beginning; transition between clip 39/40 then 38/39, 37/38 and so on down to 2/1.
If you do not want to start at clip 40 for some reason you can say do (assuming you want all clips to have transitions) clips 5 down to 1, then say 15 down to 10, then say 10 down to 5 etc etc. But you will notice that when you do clip 5/6 in this scenario you already have a transition for 4/5 so you will get an audio glitch for 5/6.
The solution here before doing transition 5/6 is to split video at playhead somewhere in clip 5 so that there is a break in the transitions but no interuption in the video.
If you are able to apply transitions in one session then working backwards from the end is the easiest solution and takes no longer than any other method.
If you have to do it in segments still work backwards but spit clip at playhead as above when approaching an already applied transition in order to create a "transition break".
Alternatively a quick and dirty way might be to split every clip in 2 before applying transitions and apply the transitions anywhere except at the splits.This way you should not have to worry what order or direction you apply them in.
If you try this let me know how you get on.