I think the main reason for this is that the Z coordinates for all the zone and safe points need to be divided by 10. E.g the safe point for qeynos2 is 31, it needs to be 3. I've modified all of the coordinates in this way, and they seem to work OK so far (I've only tested Qeynos so far, but the safepoint is now in the right place, rather than 20ft in the air near the gate, and the zone points actually go to the right place rather than putting you at the safe point)
I've put the modified zone data on my site, you can DL them here -
http://www.edwardpinniger.bctalk.net/eq/zone.txt
http://www.edwardpinniger.bctalk.net/eq/zone_points.txt