I'm having the exact same problem with the origional game. I haven't tried TFTD yet, but the only way I've found to take down a UFO is to keep my cursor where I think the attack buttons are and start spamming mouse clicks as soon as I get in range of a ship. This is a tricky proposition at best. Not sure if this makes a difference, but I seem to be running the Gold Edition, not the CE. Anyone have any ideas on how to fix this? I'd love to play a few non-terror site missions!