Since I started playing WC3, every time I load a mission my wingman's ship crashes and burns right inside the carrier. What's happening and how do I prevent this?

Too high cpu cycles in Dosbox?

I realize this is a good few years later, but I have this exact problem. For me it was fine when using keyboard only, and it started happening when I changed to mouse (due to the keyboard lack of responsiveness bug others have reported).

I don't know what the cause is, but I found a workaround. When you start the mission, begin mashing the autopilot key. This means that the instant the mission starts you will automatically launch from the carrier, saving your wingman's life. Once in space everything goes smoothly.