I know there are plenty of people getting this error and wanted to start a thread because there is so much info to wade through. I downloaded the entire game from the cryptic patcher with the file here: star_trek_online_setup.exe - 1.82 MB
Then while in the launcher clicked options and selected verify files and safe mode, and it booted up fine. Then after that I can launch without being in safe mode. I know alot of people are doing OS wipes to fix this problem and wanted to put this out there as a possible alternative.
EDIT: Ive also figured out that the game only becomes unresponsive when I try to put it in fullscreen mode. Maybe since im trying to put it in HD resolution it is messing it up, so maybe try to uncheck the fullscreen option when trying to launch your game.