Yes, the PGS/CGS committee is completely different from the Vanier committee. They are unrelated and that's why you have to send in two different applications. In theory you could get the Vanier result ahead of the PGS/CGS one, but it makes sense that you get it after since the evalutation process is longer with Vanier. Maybe in previous years Vanier's selection has been made more rapidly and they had time to let the tri-council agencies know.
Got my PGS/CGS response last week, waiting for the Vanier one!