Welcome to the forum Jeeptree.
I am by no means an expert, however I do own a few R9's that I shoot as well as shoot every single weekend in other endeavors.
12 malfunctions out of 50 in totally unacceptable!
A handfull of scenerios come to mind. Anytime I test a gun, I take as much different ammo as possible to see which will work best. In an auto, I will even alternate different brands and types just to test the reliability of the firearm. Of course as you stated, you did not have this luxury.
For an auto to work properly there needs to be a paradoxical situation in place. One a very steady platform (grip) for the recoil mechanism to work against and two, a smooth, low drag working of the recoil system; i.e. proper lubricattion and heat control. Thus, rock solic vs. slick.
From your description, without someone else being there to evaluate, it would seem prudent to me to look in these areas:
1) Ammo- as KJ reccomended, try some Gold Dot , it's like steak to these pups. If you can, try some other brands as well, maybe, Remmington Golden Sabre and Winchester White Box -ball ammo like at Wal-mart and even Winchester Personel Defense or Silver Tips if you can find it. Federal Hydra Shok are good also.
2) You said you had a firm "stance", are you sure that your wrist was locked? Or extra firm. Some people have a hard time translating these words into action. If you have to, lean in to it a little that is fine, I do and it helps with control.
3) Is there proper lubrication? Not dripping wet, but a light film on the barrel and slide rails and underneath the slide where it cocks the hammer.
4) The catch all- Dreck/inspection Is the feed ramp clean? , The extractor? No clothing threads, dust bunnies,metal shavings,anything to slow down or impede that smoothness?
5) Did the Magazine stay seated firmly during the whole shooting session? Sometimes the latch can get bumped, If the mag shifts, then things won't work right.
6) Make sure you don't go ape with back to back to back firing strings. This gun will overheat and malfunctions start showing up.
These are just a few things off the top of my head. We have a lot of experience here, I am sure others will offer good/better advice as well.
Good Luck and please keep us aprised.