I'll be honest, I have no idea why this is. It's probably something to do with how SRPG Studio handles conversation sprites. I'll look into it, but I might not be able to fix it in any sort of timely manner.
Edit: For some reason it seems that the right portraits were set to display 50 pixels below the left portraits. I have no idea how this happened since it's not like this is the default and I haven't touched the screen that changes that ever, but I've put out the hotfix for it now.