Frank Bushnell says:

One possibility: Old rolling stock has wide wheel flanges, which cause problems on modern track switches (points on this side of the pond) which are designed for modern loco and car wheels with small flanges.

So if you have old locos, find some old switches at a model fair (take sample wheels with you to check), or if you are very clever, grind out the frog with something like a tiny circular saw blade on a dremel type tool.

Newman Atkinson says:

Ensure that your rails going into the switch have as much straight rail as possible to avoid sudden changes from a curve right into the points of the switch rail. Ensure the point rails are firmly pulled into position and the switch rail also holds the wheel clearance through the whole rail. I had got a hold of an old homemade switch that worked fine in travel but the but it was a bendable rail switch as some actual proto types do today. But the rail did not hold the clearance through the whole movement. The same applies with the point rails as they come from the manufacturer. The switch was fixable and is working fine now. from Newman

Finn Sartor says:

with older rolling stock the wheel tyres are wider and there is a differents in the flances compaired to never rollng stock. I have replaced the wheels , in some cases fittd new brass bearings for the wheels and that sorted the problem. Also sorted the problem with short outs on the frogs and point rails . Bachmann do some nice wheels that fitt most rolling stock and Hornby do some nice once too.
this will save you a lot of work filing and cutting and then finding you have to replace the points .
Good luck with it , hope this answers to your problem.

Bob Roth says:

A question I have not seen asked is what is derailing? Is everything derailing, or just a few selected locomotives and cars? I strongly recommend you obtain a gauge from the National Model Railroad Association (NMRA) for your scale and check the wheels and gauge on your rolling stock that is derailing. One problem I have seen is where some of the newer cars have been manufactured with a different type of plastic in the axles and the wheel sets have gone out of gauge (it does not take very much) causing the cars to readily derail at switches. You need to check the gauge between your wheels, the depth of the wheel flanges, the width of the tread on the wheels, etc.

You also need to check your switches where things are derailing. You say that you looked at the tension on the Atlas switches, but do the points close against the stock rails? Is there any crud between the rails that prevent the points from closing completely? If the points do close snug against the stock rails, are the points bent or worn-down where they allow the wheels to roll over top of them? Same for the frog – is the point bent or worn-down? Do the wheel flanges ride over top of the frog? You might check the gauge of the track thru the switch if all the wheels are in gauge.