I forwarded your post to Dave Olson and just got a reply which I will paste here.
"Looks like the problem was found to be the truck screws. This is a good catch as the Legacy PA locos are just about to go into production and use the same or similar truck style.
I spoke with Dean in service. We don’t have any replacement screws with the counter sinking. So you’d have to find the correct screw with counter-sunk head and test it.
I will make sure this doesn’t happen on any future products."
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I do not have any of the Gilbert rerailers on my layout but figuring as Marty stated that they are most likely metric, I would measure to find the size of the screw that holds the side frame. I would then try to find a flat head screw as close to that size but not smaller, and re-tap the chassis and carefully countersink the side frame holes. This would involve a bit of work but should solve your problem with the rerailers.