Is your painted shader's projection set to Plan Y? If so, everything should line up (well, almost...). With other projection modes you'll run into problems because the displacement causes the terrain to be in a different place when it comes to apply the colour (because they are computed at different places in the displacement pipeline). Plan Y should be OK though, as long as the displacement is along Y. But if you terrain is far from 0,0,0, it may not be displacing exactly along Y and that could also explain the difference. I'd like to see a .tgd if possible.
Matt