what causes game to minimize to desktop during battles?

AgentXIII: Try checking your anti virus or anything software that may give notifications to your task bar.  Many times something running in the background wants to tell you something so it minimizes your full screen applications. As stated above, this could be caused by Java (or any software wanting to update), as well as Anti Virus. If your Anti Virus software supports a Silent or gaming mode, try turning that on.