Firesoul, yes I think I can get the neutral coop problems nullified.
I'm working through the mission list, still about 7 missions to go, most problems seem fixable so far.
There is one significant issue with the revised anomaly mission. As we've all suspected, anomalies are simulated by completely destroying your engines then 90% restoring them when the effects are supposed to wear off. Of course, that has no impact on drones, shuttles, fighters, phaser capacitors, etc. but it has disastrous effects on weapons that have a holding cost. IMO this is almost impossible to balance across the races. So, what I've done is rework the anomaly to randomly target different ship systems. One time it may hit your labs, another time the engines, another time the cloak (if you have one) another time the transporters, another time the shuttle/fighter bays, another time the shields, another time you weapons, etc etc. The effects will usually disable the system for 15-45 seconds, then you get a 1-2 minute breather before another system gets hit. It has been corrected so that any leftover anomaly effects should now get repaired at the end of the scenario.
dave