Dominions could only handle 119 sites!
According to the log.txt, Dom3 was going through the sites, and then... and moved on, mid-way?
Loading magic sites sitemod.dm
#name site 998
...
...
#name site 875
#name site 874
#name site 873
Loading nations sitemod.dm
Loading general sitemod.dm
There were sites all the way to 857.
After that, the sites show up as nameless fire sites without any features.