This construction always causes consternation and no end of disagreement. This is my understanding of the way English grammar works.
It is never correct to use a single separating comma between the verb and the predicate nominative. Surely no one wants a comma in the following examples.
...My name is Margie.
...Her response is that she was not home.
...My question was how long he was there.
When the predicate nominative is asking a question, (which is not particularly good grammar), I do not know of a separate rule that allows a comma to separate that question from the main part of the sentence. I would like the use of a comma between the verb and the predicate nominative explained from a grammar standpoint. How is it okay to put one separating comma in the middle of that sentence, which we do not do in the previous examples? How does the question there change the rule?
...My question is where did you go?
...My question is were you all there?
There is a rule that says that, when there are two parts to a sentence, one that is making a statement and one that is asking a question, it is the part at the end that determines the terminal punctuation.
...My question is when did he arrive?
...When did he arrive? is my question.
Happy punctuating!
Margie