Hi Jackson, this is based on old experience as i no longer play starbound, so i might miss the point here. You are the first in the years i've supported this mod that mentions this problem. I am therefor making the assumption that it can be 1 of 2 things:
1: There is a difference between ship teleporters and normal teleporters. The ship teleporters are normally not craftable, this is why i put a generous supply of them in the initial shiplocker. Could it be that you are using the "normal" teleporters on the ship? Especially as you mention modded teleporters, i would assume that they mod the planet teleporters, and not the ship ones.
2: If not the above, i would assume its caused by the mod, going by the lack of reports of this problem before yours.
I am aware that there's a lot of assumptions i'm going on. If I'm missing the point on any of them, feel free to let me know. Although i will not go back to starbound to extensively test compatibility with other mods (i simply dont have the time for that anymore), i'm willing to help brainstorm other possible solutions.