Ive noticed that the only way I can get to the launcher at any time after I select the EXE file to load is that I have to load up Freespace and then quit and then delete the 3.6.9 exe process in my Task Manager. After I end the process, a box named "Failed to Read Flag File" pops up, I click OK and then the Launcher appears and when I look at the Feature tab - its all blank.
There we go. I now know WHY you're having this problem. Let's see what we can do to fix it. For some reason, the .exe isn't responding correctly to the launcher's request for a flag file. Instead, it appears to be starting the game. So here's what you do. You hit the start button and go to "run..." You then type in "cmd /k cd C:\Games\FreeSpace2\"
When the command line window comes up, type in "fs2_open_3_6_9.exe -get_flags" and tell me what happens.
EDIT: Well, that explains why it was having trouble with the flag file, doesn't it? Oh well, problem solved. I'll leave this post up for anyone who comes later and needs this help.