Hello Vijay,
Would it be possible that you send a scope shot of the startup? I wonder if the part does not start at all or if it tries to start and the protection kicks in. If the protection kicks in, please check if there is one output voltage that drops in voltage after all voltages reached already their final value.
Another test would be to check with TPS65101 if the problem is gone. This is the same part, just the boost converter has more current and the protection is not present, so it could be used to check if one of the output voltages falls out of regulation and which one.
Best regards,
Brigitte