All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
As for the question on whether or not obedience to the one who orders you to commit sin is Shirk, the answer is that it is not Shirk in itself as long the one who obeys does not hold the belief that the one who gives the order reaches the status of a "legislator", (like Allah and His Prophet) Who must be obeyed, and as long as its doer does not make it lawful for himself to commit such a sin as a result to his belief (that it is from a legislator).
But if it is not accompanied by what we mentioned, then it is considered a double sin, not Kufr.
So, if you do not pray Fajr and ‘Ishaa’ prayers in congregation as a way of obeying your mother's orders, you will not be considered a Mushrik, as you do not consider your mother a "legislator" other than Allah. But you have made a mistake by obeying her in that matter.
Allah knows best.