Final answer:
The secret that haunted Charles for 50 years was his childhood of working in the blacking factory.
Step-by-step explanation:
The secret that still haunted Charles after 50 years was a) His childhood of working in the blacking factory. This is evident from the passage that mentions the 'foul stream of hereditary evil' running through him, which refers to his difficult and unpleasant experiences working in the factory. Charles felt the burden and shame of his past, and it haunted him throughout his life.