Whenever I enter a battle the Sunrider sprite would not be visible. I know its somewhere because when I would auto-formation and try to move one of the ryders to the center hexagon it wouldn't let me. Completely vanilla steam version.
Are you finding that this is occurring on specific ones (in particular the ion storm (mission two)) or all of them? If the ion storm and you're using auto formation this is because it is a developer tool that wasn't really intended to be used by players (but was left in the final build) leading to some unusual side effects (such as accessing units you shouldn't usually get).
If it is happening on all missions try using'shift + g' while ingame or holding 'shift' when launching and changing the graphics rendering option, I recommend the following order:
#1 - OpenGL #2 - DirectX #3 - Software
After changing this setting remember to relaunch the game.
Be warned, elements of this post may have been influenced by my 'West Country Logic'.