Do not remark the rune before you have drydocked the ship. Or the problem will return. Drydock the ship first.
If your ship is experiencing this issue, then you MUST drydock it and then launch it again. You will receive a new pair of runes for it, and thereafter any additional runes you mark for it will not become broken.
If you do not drydock and relaunch the ship, any new runes you mark for the ship will lose their link to the ship during the next maintenance, and the problem will continue.
Newly placed ships and ships placed from drydock will no longer experience this issue!