I have a question, when I am test running my missions, when I engage the enemy ships, they often just fade out of existence, meaning i can't complete the kill objective. Anyone know why this is happening? I have the behaviour set to True Combat.
It should be fine. There are a lot of inconsistencies between the live game and in-foundry test runs. Path finding, for example, is also much better live than in the foundry. On the other side, some things will work in the foundry and not on the live game. This is why it is important to do test publishing and running the mission that way.
I suggest giving it a non-title such as "Test X1" for such run with a request to not play it in the mission description. Just wait until you are ready to do the live test run to publish and take it back down right away. You can publish, take the mission, and then unpublish before playing as well. If your character already has the mission you can still play it even if it has been subsequently unpublished.