Well to start, acetone is polar which means it will dissolve in water. Your DMT is now both inside the acetone and the water. The reason we use naphtha is because its non-polar, and it does not mix with water. When the DMT is released from the mimosa cells, it dissolves into the water. When the floating DMT is caught within the naphtha, it can not escape back into the water.
I don't really know where to go with this. I would say you need to get more naphtha to extract with, since it won't mix with the acetone. Somebody else can probably provide better insight, I've only extracted less than half a kilo of root bark at this point. I don't know what kind of harm, if any at all, was done to your DMT by adding acetone.