JMW uses the BSP's 0 0 0 as it's center of origin. this means when animating it in max, you would need to place the dropship at the BSP models' 0 0 0 center for it to look right in game.


Personal note...
I never liked JMW, it's trippy. I just used a regular JMM then placed the vehicle the closest I could get to the reference in max. Seems to work :S.

JMW teleports back to origin after it's done too, which is what's going on with you right now. Can't think of a way around that.