I used the latest source, but azone2 hasn't changed for a couple of years, certainly not since the Windows executables you linked where posted.
Your output should be exactly the same as mine:
http://www.rama.demon.co.uk/bloodmoon.txt
in particular, the bit at the bottom:
Code:
After processing placeable objects, there are 2022930 vertices and 674310 faces.
Bounding box: -1276.30 < x < 1648.32, -572.67 < y < 1168.28
Building quadtree.
Done building quad tree...
Match counters: 3435858 easy in, 10165604 easy out, 3770 hard in, 0 hard out.
Writing map file.
Map header: Version: 0x01000000. 674310 faces, 788 nodes, 711249 facelists
Done writing map (36.17MB).
Dumb question, but I have to ask

You are copying the newly generated bloodmoon.map file into your server Maps directory ?
You can verify this, because in the zone log, you will see:
Code:
Map header: 674310 faces, 788 nodes, 711249 facelists
Loaded map: 2022930 vertices, 674310 faces
Map BB: (-1276.30 -> 1648.32, -572.67 -> 1168.28, -146.18 -> 459.89)
Map ./Maps/bloodmoon.map loaded.
which matches up with the output of azone2 when the .map was generated.