You either have another ship mod installed, or installed the mod after you already created your character/ship. Either way, the troubleshooting should still fix it. copied here for your convenience.

Troubleshooting

start the game, play your bugged character, and close the game
go to starbound\storage\player
sort by date, and rename the latest .shipworld file to .old
then start the game and start your character

If there are still problems, let me know the following in your post:
* What version are you running: see in start screen, click the gear bottom left, and look for the version number*
* What race you play, and if not vanilla if you have the appropriate addon.
* What other mods are running besides BYOS
* If the update does not work, make a copy of your starbound.log file so it remains intact before restarting the game, put it on pastebin and include the link.
Please describe if you did anything else to your ship/mods/game that you think might be of interest.

I forgot to mention that I did install the mod after starting the playthrough. And I did the troubleshooting process, but all that did was reset the ship with a ton of rooms and cause the two crew members to comment on non-existence being scary.

What race are you playing? And what other ship mods do you use?

for your info: at the start of a playthrough the ship is recorded up until the highest tier. My mod replaces that base ship for all of the base races. If you have ship mods installed, it will again overwrite my byos ship. If you are playing custom races that dont have my replacement (so do you have the byos addon for that race installed?) it will not have replaced it because it doesnt know what to replace.

Solution for the shipmod:
disable the shipmod, do the troubleshooting. Reenable the shipmod and you are good to go

Solution for customrace:
start a vanilla character, do the quest, double check that it works, and then just copy that characters shipworld file over your own.. that should also do the trick.

Hope this helps.

That second solution worked! Thank you.