I don't know if your problem is related to mine, but If the ctrl key is pressed while loading DCS, the activation window(s) will pop up. In my case, I had my TeamSpeak push-to-talk mapped to ctrl-ins (or something like that). If I happened to be talking on TS as the game was loading, I kept getting these windows popping up. Drove me nuts until I figured it out. I fixed it by simply changing to another TS key combo that didn't use ctrl.