I have a new version up with more improvements for you all.
I cannot work out what is causing the expansion to fail when playing with 4 people, there are no errors in logs that have been provided. I also ran a test with myself and 3 AI characters (which causes 4 ACUs to spawn) and it worked fine. If this issue starts reproducing often, I will investigate further. For now I have concluded that it's nothing to be concerned about as of yet. The mission now ends, it no longer plays the winning dialogue twice.
I've changed the drops for the second part of the mission to stop transports flying over the civilian base with no units on-board. As suggested previously, I have removed the direct teleport when a quantum gate is constructed. The Cybran Commander now targets random structures instead of the player ACU directly. I've also removed some code that caused him to become invincible when he warped. He's now prone to death like the rest of us.
Some attacks have been added whilst the truck delay is active to encourage the player to defend the facility whilst the trucks are being loaded (I don't want the mission to get boring).
For future versions, I plan on adding some more attacks to each AI and using more functions available to make it feel more like a mission that GPG would release. Thank you to all of you that provided logs and additional feedback, it has helped develop the final stages of this mission. Let's hope that this brings it to a playable state that's suitable for release.
In the next couple of weeks, I will be making a start on a new mission for a rebel campaign that I have planned, so keep your eyes out. For now, if you wish to test or play this mission, you can find it in the original post like before.