[lugerholsterrepair]

I do not believe you will trace a failure to extract to the magazine. From what you say the magazine has performed admirably. It's function is to bring the cartridge into position so it can be pushed into the chamber. Once the cartridge is chambered correctly the magazine is irrelevant. The cartridge has left the realm of one system and entered another. It cannot be more plain that once the cartridge is in the chamber..it's failure to extract has nothing whatever to do with the magazine..empty.. or pregnant with cartridges.
My suggestion would be to closely examine the condition of the extractor before every shot. Be especially observant of the shots you know or suspect might fail to extract. On a normal extraction you will observe the extractor to be at a certain angle. If you observe an abnormal angle..either too low or too high something is amiss.
The extractor must be just right to lay in the extractor groove. Too low may mean the extractor has not been pushed far enough forward to rise above the base of the cartridge base and fall into the extractor groove. You could then notice the bolt face possibly pushed away from the rear of the breech in this case exposing a glint of the brass cartridge.
If the extractor is too high it might be riding on top of the base of the cartridge. Either of these two conditions might put the pistol slightly out of battery but still able to fire.

One other consideration is to check your headspace. It is possible that your headspace has been eroded enough to push the cartridge into the barrel too far. If you have a strong extractor spring the face of the extractor could simply push on the base of the cartridge without riding up and over the base into the extractor groove.

All of these scenario's could lead to pierced primers. If the cartridge is away from the bolt face apon detonation... the base of the fired cartridge would slam back into the bolt face with abnormal force resulting in inertia overcoming the firing pin spring causing the firing pin to be fully forward in the bolt face..piercing the primer on occasion .
It would be good to not only examine the angle of the extractor but to keep track of any shots that result in a pierced primer.

My advice is to make absolutely certain of the headspace..IF it is eroded and out of order enough to cause all of the above it is dangerous not only for these reasons but for the fact that if a cartridge is pushed too far forward into the barrel there is a possibility of the bullet being trapped in the barrel and abnormal pressures are the result.

One thing to remember is..pierced primers, overly flattned and loose primers..all indications of HIGH pressures.