My guess here is that with those settings you're probably effectively turning CV off and that's why the problem *appears* to have gone away.
Back to your OP...
Using CV I get a clunk from the motor on the z-axis (probably losing steps) on a lot of the G00 moves to up safe z which preceedes a G00 move to a new A.
The thing of interest here is that CV is not (or should not) be doing anything anyway in this situation because it doesn't (or shouldn't) blend a rapid into a rapid.
In the three lines you've shown, the only blend should be between the first two lines and even then it's a "straight" blend (Z into Z)
what happens if you put a a zero length dwell (G4 P0) bewteen 680 and 690?
Ian