Hi alex,
I think perhaps you are missing a step for the particle FX. You need to make sure you save your particle system as it's own prefab first. Dragging a particle system from your scene into the Module FX library won't work properly... Try the following...
1) make a new prefab somewhere in your project folders.
2) drag your particle system onto the prefab to save it, and give it a unique name.
3) in the Module FX list click the 'Add New System' button
4) drag your Prefab into the slot.
5) play your scene once and then stop, just to make sure the new particles get registered.
Once you do this you should now see this particle system showing up in each of your fx_object lists.
The Preset Transition API is currently disabled, unfortunately, as there were some bugs that were recently introduced. I'll make sure this is up and working for the next update.