Hmmmm, well I just redid the waterpro without changing the main water level from 6.0, and it worked just fine when I used the 'generate small map' button. Steve, test out a boat in the water on the last version I posted, and you'll see that the physical and visible water are both fine, it's just the boat wakes that got screwed up. It almost seems like the black bits in waterpro just don't work if you lower them.
Anyhow, I suppose it doesn't matter now, as I've already raised the map and path coordinates three units so the water works, and is compatible with Barton's mission script. It went rather painlessly as well since I wrote a quick PHP script to raise everything for me.
Get the updated v03 paths & illcom .ipl's, and new waterpro file right here
Or, if you haven't installed any of it yet, get the full v0.3 package over here
And if anyone has installed, or is working on any additions to the map, be sure to raise the Z coordinates for all new objects by 3 units to match! If you have lots of added objects, and don't feel like adjusting by hand, send me the ipl, and I'll fix it with my script.