This morning i tried to start the game and all it did was open the task but nothing happend, i could see the window but it wouldn't open up. No idea why it started to happen but it did. Tried nearly anything, from removing anti virus to restarting, uninstalling, etc.
In the end i found a solution that worked for me.
> Opening Star Trek Online so that it would sit idle....
> Open Task Manager
> Right Click on the STO Task
This is what made the window pop up on full screen so i could atleast see the window again and log in. I hope this is of any help to the developers and other people having the same issue.