My application got flat-out denied because my graduate GPA was not being considered at the time. Unless NRD Miami was completely misinformed a year ago, it is entirely possible that only until recently have they been considering your graduate GPA as well.
At the time of my first application, my OR was also confident that the graduate GPA was to be considered as well and it came to us as a surprise when it bounced back.
Who rejected your application? The selection board? They would certainly know that Master's GPA would be considered. Maybe they're disregarding it if you haven't finished your Master's yet?
Here's the thing with SWO:
1) They get most of their accessions (like 75%) from NROTC, USNA, STA-21, and means other than OCS. As you can imagine, this makes OCS applications for SWO very competitive. This leads to number 2.
2) SWO is the NROTC/USNA "dumping ground" for lack of a better word, hence why they're such large commissioning sources for the SWO community. If you get through ROTC/USNA, you have to serve, but if your major/grades and other markers aren't up to snuff for any particular designator, people typically get thrown into SWO. This also makes OCS applications for SWO very competitive.
3) It's the Navy's bread-and-butter designator. There's all kinds of different kinds of job you can learn and do while on the job and so at least from the officers I've talked to, they want them starting young so they're more easy to get into the mold. I'm a week from 27 and was told my age would be a bit of an issue were I to apply for SWO (active duty) as opposed to other designators (as I'm in the process for).
TL;DR: SWO is easy to get into via NROTC/USNA, very hard to get selected for OCS.