I'll still stand by my assertion that it's because of the scale setting.
It's easy enough to test. Lay a section of track. Select a PBR texture and paint under the track. Using the same texture change the scale setting and paint over a section of the previous painting. You should see the effect in your original screen shot.
If using different PBR textures, as you have, you may need to modify the scale setting of one of the textures to avoid your issue -- a scale setting of 1 for one texture might not be the same as a scale setting of 1 for another texture. Experiment.
Phil
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Edit:
Just done a bit of experimenting. I downloaded your City textures (they are excellent, by the way, but do lack a winter snow texture). For some reason they do not match the other PBR textures I've been using, no matter what scale settings I use.
In my layouts, for example, I've never had any issues with, say, PBR Mud Dry 1 - Seasonal (one of my favorites). It works perfectly under the track with PBR Foliage 3, PBR Gravel 2 - Seasonal, ... provided the scale settings are the same. But I can't get any of those PBR textures to work with any of your textures.