if this isn't your install directory, there may be missing files which have been installed/patched to their default locations instead of to your custom directory.
also: is the server online? sometimes the login screen shows server as up, but server is actually down, hence no connection.
Comments
what's your operating system? where is the game installed?
for vista/7 the install directory should be:
"C:\Users\Public\Games\Cryptic Studios\Star Trek Online.exe"
for xp it will be:
"C:\Programme Files\Cryptic Studios\Star Trek Online.exe"
if this isn't your install directory, there may be missing files which have been installed/patched to their default locations instead of to your custom directory.
also: is the server online? sometimes the login screen shows server as up, but server is actually down, hence no connection.