I am having this same issue. Whether or not I actually command the battle or auto resolve.

Also having this issue. My temporary solution would be to leave the planet with Thrawn on it under siege to prevent the Empire from building ships on that planet. Or just find his xml file and change the Tech Level to 99.

same here

yeah, thrawn doesnt appear on the battlefield either (in space i mean) so im inclined to believe some of his files are missing/corrupted, i think this can be fixed if you just remove everything thrawn related from the mod file.