I think what the guy is trying to say is that he gets smooth window movements and stuff when both his AGA and graphics card vertical refresh rates are set the same.
I know from my own experiments that some of the OS functions such as "WaitTOF()' don't seem to work as expected with my BVision card. WaitBOVP() seems to work OK, however.
No doubt some of these functions like WaitTOF() are tied to the original hardware and perhaps theres a sync bug in dragging windows etc. around because of this.