Sounds like you have the random hidden window problem. try these to fix
1 . be sure in the task manager no other copy of the startrekonline.exe or gameclient.exe is running
•Launch your Champions/star trek Online Launcher. It will do the whole sit there on taskbar and tray with nothing showing.
•Open up task manager (right click on task bar, select Task manager, or press ctrl+alt+del and select Task manager).
•In task manager, minimize and then maximize said champions/star trek online launcher program through task manager (right click on the champs/star online application in the taskbar list.)
or try
download
http://files.champions-online.com/Sh...herWindows.exe
this must be run as admin in vista/win 7 and run just after you launch the game.