Hey all,
Setting to software mode fixes all the CTD, you can enter your captain's name, all key commands work, and there is no screen flickering. :)
I just played three missions with no difficulty and upgraded to a Federation light cruiser.
Go into the directory where you installed Starfleet Command and look for the executable called config. Switch your graphics to SOFTWARE MODE and 800x600 resolution and you should be good to go.
Thank you GOG for releasing this!!! Hopefully we will see Starfleet Command: Orion Pirates soon as that one is considered the BEST of the Starfleet Command series and there are brilliant mods for it.
In the meantime, I have some Klingons just aching for some Federation photon love. ;)