I see a number of possibilities.

The first would be not to decide on the specifics at all, with the reasoning that the characters likely wouldn't know either. It's a post-apoc world, so people likely don't understand how modern precision guns work (or computers, and so on). Also, unreliable guns fit the post-apoc theme, so it's likely the players would accepot "unreliable guns" as a part of the game, in the same way as they accept mutants, and biker gangs.

Second, you could put this down to bad maintenance. This ties in with the above really - people don't have the machinery to properly maintain and repair modern guns, so they have to make do with what's available. This leads to shoddy replacement parts, and so on.

Finally, depending on how high-tech the pre-apoc setting was, yoiu could have nano or bacteria float around. Bacteria which eat, say, oil or rubber aren't that farfetched, so hy not have some which like gunpowder?

Here's one suggestion:
If it was a war that was the cause of the apocalypse, then you could have one country having infiltrated the other country and contaminated their ammo factory with an "unnamed" chemical(s). (In actuality a time delay combo of chemicals that only killed the gunpowder after it was mixed together for a while) This caused the main ammo stores for the military in the players home country to be unreliable, but it was a great mystery there as to why. The unreliable ammo was what caused the players country to be losing the war and to launch the final retributive strike that destroyed the world.

After the war, people raided the military supply houses for ammo, and ended up mixing the good ammo with the bad.

It got even more confusing for those living in the new times, because as the cause was a mix of chemicals, a sometimes mixing the powder from two good batches resulted in the new batch containing the right combination of chemicals to make the whole batch bad.

As most everything found today is scavenged, much of the contaminated powder is now mixed with the older "good powder". As such much of what is available for modern firearms are questionable at best. Some bullets work, and others in the same batch (because of an unlucky combination of chemicals in the powder) do not work.

You could simulate this by giving a flat % chance for a given bullet to fail. So every time they shoot a batch of powder they didn't create themselves, there is a chance that they get something that destroyed the effectiveness of the ammo.

Well, the basics of the setting are that the apocalypse was a simultaneous nuclear strike caused by a ritual releasing the four horseman. Of course, I could easily chalk it up to the horseman of War simply not liking modern firearms and magically disabling combustion...but that is a bit TOO much "a wizard did it!" for me. I wonder, how easy is it to mix smokeless powder without modern manufacturing facilities? It could easily be that they simply do not have the resources to make more and have switched back to black powder due to ease of manufacture.

There's lots of ways to do this (I really liked Zorg's idea of bacteria corrupting the supplies).

Putting the blame on the chemicals, this could be because:
- Stock that is unreliable due to age (Scrub-kai's basic premise)
- Poor manufacturing standards for the chemicals (rather than the weapons)
- One essential chemical is of poor quality, due to coming from an unreliable sources (e.g. mine) or knowledge of how to refine it has been lost.

All of these last leave the possibility of there being a pure (i.e. reliable) supply available somewhere (e.g. a well preserved stock; a mad scientist who knows how to produce the pure chemicals; or a mine contain a pure vein of the required mineral) if only the party can find it.