In particular 1.5, when i duped a layer that had particles on it, i got an exact dupe - same number of particles in the same position.
Now, not only do i get a different arrangement of particles, but the particles on my original layer shift as well. It seems to be using the layer index as some sort of random seed - even though the keyframable random seem attribute doesn't change.
Any way to emulate the 1.5 behaviour in 2.0, and not have particles change when moved in the stack?
I wish I could help. When I duplicate my particular layers, everything lines up perfectly. are you sure you dont have anything on the layer or in the settings linked to the layer number? That is the only thing I can think of.