Hi Khatarah!
This is a known problem. I tried the FSX demo when it first came out and posted this
problem here. I don't have FSX yet, so I can't help.
FS2004 works find in Local mode with TB. If you use TB with 2 computers in Network mode your problem will not occur because your touchscreen will be on another computer.
This is really not a TouchBuddy problem. It is a general problem with FSX. If I were you, I would post on some FSX forums and just ask "Why does my 2nd Monitor go black when I play FSX?". I'm sure there are other people who have a second monitor and wish it would work while playing the game.
WBK