It sounds to me like you made the same mistake I did orignally and painted the tracks with enamel paint. If this is true, enamel paint will not adhere to vinyl tracks and will usually end up coming off at some point in time. If you paint with acrylics, this shouldn't be a problem.
I now primer coat my vinyl tracks with cheap black acrylic artist paint (.99 cents or less at most retailers). Once this is completely dry, you can paint, drybrush, and weather the tracks with enamels or oils without fear of the paint flaking off.
Hope this helps.
Foster