What you have pointed out is illogical in the legal sense of interpretation. Whenever two separate codes or statutes are concerned over the same subject matter, a harmonious construction is supposed to follow.
Here, you say the Central act does not lay any limitation on the registration of the stamp paper after the payment of duty while the Bombay act imposes a limit of 6 months. Here, it must be understood that the Central Act is merely silent on the said aspect while the latter has expressly provided a limit and isn't in contravention to the Central Act at all because it is not expressly mentioned in the Central Act that there shall be no such time limit. States are free to make their own laws and rules within the framework of such Parent Act and thereby, the limitation of 6 months is a valid measure, and the same will prevail to the areas where such act applies.