Dead AI on the map is caused by drops from mission and ALTing out. I ask that people do not ALT from missions unless absolutely necessary and refrain from running software firewalls.
The test I just ran at home does not indicate failure in AI creation due to settings or shiplist. The shiplist issues I found are a few spaces here and there and some odd issues with fighter model pointers, neither of which should cause these issues.
The SQL db must be corrupted somehow, I suspect by editing the terrain on the live server or other admin character edits that were not anticipated. It is also possible that the "attack your allies" missions are not destroying mission AI on completion for some reason...
I will inspect the SQL db for corruption, clean it, increase AI destruction settings, pull the HBConvoyRaid that I missed and try again. If the issues persist we can look at pulling the "attack your allies" missions or falling back to the flatfile.
Bear with me, we shall press on.