1. Technically, the Railway is right not to accept your resignation when disciplinary proceeding is pending against you,
2. It is surprising that the Authority allowed you to rejoin them since as per its Service Conduct Rule, you are expected to be suspended till the enquiry is over,
3. Since the charge against you does not have any financial implication, they should quickly complete the enquiry and award punishment either warning or termination,
4. Moreover, if you have not yet been charge sheeted, then they should accept your resignation letter,
5. Even if disciplinary proceeding is pending against you, they can wind it up on the ground that you have already tendered your resignation,
6. You can file a Writ Petition before the High Court praying for appropriate relief.