The AI file issue was due to new additions that I had added in the scripts that only work with the 1.12 se5.exe file. Anyhow I've re-posted v0.94 with working empire files for SE:V v1.08
Updated v0.94:
http://www.captainkwok.net/balancemod.php
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AAshberry: Did you notice if they had ordnance or not? The other explanation is that the leader might be getting hurt and the fleet is not breaking formation. I'm going to do some strategy tweaking to fix stuff like that today.