Due to an unknown cause, all rail entities on a ship will stop updating. This problem persists across servers and is carried in the blueprint. Copying sections of the effected ship and pasting them onto a new core will carry the problem with the pasted section as well. (Only tested with sections that contained rails\logic.)
The only known workaround requires the removal, replacement, and re-linking of ALL rails\logic in a build. I have had multiple people, on multiple systems try this and it seems linked to the blueprint\ship.