I have to be careful with the Shinohara track I use. The paint is reasonably durable but will flick off if scraped or prodded.
Did you wash off the ties before laying the track? There is probably mold release agents (silicone) remaining on the plastic.
It may not be easy now that ballast is in place but for any future track laying I'd suggest a wash in either a detergent or strong alcohol prior to painting. Perhaps Windex, Simple Green or Fantastic (experiment) then blot off the excess and allow to dry.
The paint should adhere reasonably well but it won't be perfect. That's the same plastic used for truck sideframes and diesel handrails.
There are bonding-primers for improving adhesion to plastics (think car bumpers) but that may not be completely necessary.
Atlas, at least the stuff I have, seems to be molded with a different type plastic that accepts paint much better.
Good Luck, Ed
