Replace With After Effects comp causing speed changes to the top layer?

I am having issues with Premiere Pro and Creating linked After Effects comps.

I am trying to motion track a plate shot into a shot with green screen and AE is not being nice. I was on chat support with Adobe in India and they are clueless! They dont even understand what it is I am trying to do.

In Premiere I have 2 layers. 1st layer has the scene with green that I want to track & comp a plate into. The first several comps I need to do have the plate playing at 25% speed Nested and looped. And then some of the others have the Plate layer at 1500% spedup, looped and nested. When I select the the Green Screen layer  and plate nest and select replace with after effects composition it speeds up the  1st layer.

Is there a workflow thing I am missing here? I prefer to edit the layer content in Premiere for timing then bring in the layers to AE. I suppose the problem lays in my nested speed changed plates. 

I thought nesting would have worked but it didnt? Do i need to export the plate loops and reimport as new clips?

any help would be great!