Anton, I just, and I mean JUST, got a set of Walthers RTR passenger cars, at a train show, a set of 6. Out of the 6 cars, four were bad. It seems that when you get bad wheels they come in "bunches". Mine weren't that bad, I didn't think, but they wouldn't pass the "gauge test". No difference to me anyway as I usually change to QUALITY metal wheels and I did so with these. Oddly, to make a point, these were not Delrin wheels, but metal sets. All of these cars got brand new CV metal sets.
Even with code 100 switches and track, the deep "pizza cutter" wheels climb the frogs and the rail. And if the slightest bit of ballast is lying along the inside of the rail, it will cause the wheels to "climb the rail". Back in the days before RP25, it was inevitable to buy a bunch of cars and have problems with all wheels causing derailments. Most of us back then just took it as a part of the "game".
A few years ago Atlas had some really big quality issues with their switches. The big reason I rarely use them to this day. The frogs were too tight and too high. This caused the wheels to "hang"(get stuck) causing the couplers to pull apart, or wheels to "climb" and jump the rail. Even RP25 wheels weren't immune. The problem then was the switches and not the wheels. And I did as you, I filed down the frog and widened the gap between the rail. But, that got tedious after a while.
The problem with wheels, now, is much less prevalent. The standard, RP25, has made the problems more scarce. But, problems do happen on occasion. I've found that it happens in bunches, and at random. Usually in cars of the same type and model. It seems like the manufacturers get into a bad lot and keep on running until the batch is gone. I have even gotten wheels that were flat on one side. Thump, thump thump down the rails. Hard to figure out how it made it through inspection.
The problem lies in two areas, both QC related. One, humans are involved in the manufacturing. Two, machines are also involved in the manufacturing. Both, or either, can fail and make "mistakes". But, I'd venture to say the biggest component of the errors are human. Whether it be falling asleep at the wheel, or not providing proper maintenance to the machine.........
Another point I should make. Older materials, track, switches, etc, were not made to the precise tolerances as they are today. Part of technology, I guess. With tighter tolerances, one can expect more "quirks" and "bugs". The problem with wheel gauge is very prevalent in brass models, but not as bad as years back.
But, for the sake of sanity, I would almost always suggest that one change wheels to quality metal wheels. The cars pull better and track better. And they stay cleaner. If problems do arise, it is best to check the wheel gauge, the switch frogs, and the track gauge. By doing so, one will be able to whittle down what the problem isn't and focus on what it could be. Much like trouble shooting a large machine.
The gauge sold by Kadee is one of my handiest gadgets. And it is available for most, if not all, scales and gauges of trains. I might also suggest here that the OP(original poster) check the gauge of the track at the problem areas. The track may narrow, or widen, just enough to cause a problem. I see it happening at curves usually, especially when one uses "flex", though rigid corners are not immune. And making sure the trucks are loose enough was a good suggestion. Some tighten them too tight. Have you ever sat and watched a REAL train? Ever notice how the cars sway from side to side? The same is needed on models. Maybe not to the same degree, though. I usually tighten mine tight and back off 1/4 turn, more if needed, to turn very freely.
Bob