#1 - he was not born in the Canal Zone, but a hospital in Panama.
#2 - even the Canal Zone was not considered U.S. Territory at the time under the naturalization laws.
#3 - since he was not born in one of the States, even if he had born in the Canal Zone, and even if it had been U.S. Territory under that law, he STILL would have been naturalized because he would only have been a citizen under Congressional Act, not common law.
No matter how you look at that one, he wasn't eligible at all.
I'm not sure of Rubio's issues. If he was indeed born in Florida, and if both of his parents were citizens, then yes, he would be eligible. (any laws dealing with time period of his parents' citizenship are with respect to naturalization, which would not be relevant in the case of a birth in Florida as common law makes no such distinction)