Lok Sabha and Rajya Sabha have passed the Constitution (121st Amendment) Bill 2014 and the Judicial Appointments Commission Bill 2014 simultaneously. The Bill seeking to amend the Constitution makes changes to the provisions relating to judicial appointment, inter alia empowering Parliament to pass the Judicial Appointments Commission Bill.
The constitutional problem is this: the constitutional amendment still requires the consent of several state legislatures before the President can sign it into law. Thus, the two Houses of Parliament have passed the Judicial Appointments Commission Bill on dates on which the Constitution does not (yet) authorise them to do so. The point is not merely technical. If the requisite number of state legislatures do not endorse the constitutional amendment, there is no doubt that the JAC Bill will be unconstitutional. The question is, if they do endorse the amendment, what is the significance of the fact that this Bill was passed by the Houses before Parliament had the authority to do so?
One possible solution might be for the President to not sign the JAC Bill until he is able to sign the constitutional amendment Bill into law (ie after the consent of the states has been secured). This would at least ensure that the JAC Bill wasn't formally enacted until Parliament had the power to do so (remember that under Article 79 of the Constitution, Parliament consists of the two Houses and the President).
While this would be a wise course for the President to adopt in any case, there could still be a lingering question about whether any part of Parliament is competent to even initiate legislation at a time when it lacks the authority to do so.
Update: Apparently the Minister told the Rajya Sabha that the government will not send the JAC Bill for assent to the President until the requisite number of states have ratified the Constitution Amendment Bill and it is assented to by the President.