i think valve use the clip texture for their track-train brush.
as to the bomb model not moving... i have no idea why, but i've also seen this happen on my payload occasionally - however it appears to be client side, since it will only happen for one person. everyone else will see the bombcart model move as normal. - in these cases the bombcart model will stay put but will teleport to the track train position when a point is capped, and then move with it normally.
i use a prop_dynamic like you, but valve actually use a prop_phys for their cart model (mainly so it will fall down the hole at the end). shouldn't make a difference, but i've come to see hammer as tempermental at times. maybe try copying valve and see what happens.