huh ?
FLMM is the Freelancer Mod Manager - and it does not add any ships to any game play. The mods do. Some of them removed the docking sequences, some don't. Reason: big player ships might get stuck in the station doors.

Because you speak about FLMM I suppose you use a mod. Specify please.

Yes, of course

I mean that during the base and planet cinematics when you can normally see the ship you are flying take off, land, sit there, etc. All I can see is the weapons, CM, thruster, and the engine exhaust, but not the ship. It's kinda weird. Only does it to custom ships.

With some ships, the camera is set too close and you are litterally inside the ship, like when you land on pittsburg with king, trent steps out of a custom ship and all you see is weps.

You've also got the probability of the LODranges being off or a badly fitting .SUR file, neither of which you can do a lot about without learning to mod. If you can't see the ship on Manhattens landing pad but can when your behind it in space then it's the LOD's, anything else will be the .SUR file.