First, uninstall everything related to the game. Patches, mods, new ship models, the game itself, everything.
Next, reinstall the game, fresh install using the install disc. Once the game has been installed, install the patch available at the link provided:
http://starfleetcommand3.filefront.com/file/sfc3_beta_patch_v534b_all_languages;28800Restart your system just in case, and if there are any other problems after that, we'll try and help you out.
DO NOT INSTALL ANY OTHER PATCHES!! If you just want to play the game without mods, follow the install instructions I have provided for you.