Looking only at the covers, these two issues appear to be two separate specials published five years apart. Although it is true tht the second issue has a #1 on the cover, the indicia of the second issue states that it is "Captain Marvel vol 2 #2." As the indicia has historically been the primary determing factor of series numbering, this site considers this Captain Marvel (2nd series).
The five year hiatus between the two issues was almost certainly to publish a book with the name Captain Marvel in the title to ensure Marvel retained copyright and not lose it, as did Fawcett/DC Comics.
