It could also have been caused somewhat by have to wear that chain on his ankle for so long.
pretty sure yana only draws ciel walking with a cane for the Vibes, but my headcanon-that-is-totally-canon says the cane serves as an actual disability aid
its likely he experienced damage in the cult that made it difficult for him to be on his feet for an extended period of time - clearly he can walk/run, there's just a limit on doing so pain-free
this is also part of the reason he doesnt like dancing!