Can't use ship components after researching them (for all races) on twilight

You may be using a mod or an overriding file.  Try turning off mods and starting a new game.

another idea:

the ship designer has some filter options to display specific types of equipment and hide all other components; maybe you have selected the "beam weapons" or "missile weapons" filter, so your mass driver weapons aren't displayed in the menu.

I know about the filter options up top. All other mass driver weapons show up (for my race only the railgun techs and the space cannon). For other races, the scatter gun, singularity driver, and the nano ripper techs also work fine.

I'm not running any mods either, the only thing I ever did to change the game was make a custom tech tree while not altering any of the other ones. I just copied one of the others and altered it and named it something else. I don't think this should effect anything, as its not overriding any files, just adding an additional tech tree. I have also used this custom tech tree before without any problems, and I tested out the the other races using their respective tech trees; same problem. For other races, the pulse cannon techs also do not show up.

I tried uninstalling twilight and re-installing it, but it didn't change anything. So I think something is wrong with the core of the game itself, or something's wrong with the twilight files located under user, which aren't deleted when the game is uninstalled.

No idea whats causing this. As I said, I played this game awhile ago with my custom tech tree and had no problems, and never altered the game with mods or moved things around since then.

You should probably try backing up your user data to another folder and see if a blank slate fixes things.

Fixed it. Something happened to the core game data. Uninstalled entire game and reinstalled it, now the components appear in my save games. Still don't know how that happened.