Same problem here. In previous generation fglrx (up to 8.40.4) the ~/.drirc file worked perfectly for setting vsync.
Now (with fglrx 8.42.3) the vsync settings can *only* be applied in amdcccle, and don't survive a reboot (although amdcccle stores them in /etc/ati/amdpcsdb and remembers them).
Another thing I noticed, is that vsync happens too late (when about 20% of the screen is already drawn).
Has anyone tried to "strace amdcccle" and see how it communicates with the driver when pressing "Apply" ? If we find it, then I can write an automated program to apply any settings, and auto-start it in kde or whatever :-)
I haven't found anything but, yes, vsync has problems. I don't see it at 20% of the screen like you say, it more like fluctuates in and out from where it should be. That's nothing new in this version though. Been that way for me since I first used the driver. Can't say for sure if it got worse, but it's likely.