The extension adds layers to the base image layer. Anything that was added to an image without the extension - modules or campaigns before the extension was enabled, will have the links and tokens on the bottom layer, because this is where they were placed.
This is mentioned in the gotchas and information in the first couple of posts of this thread.
I'd recommend you delete the tokens and re-add then to the top layer, and just go to the bottom layer when you need to select links.
I'd also recommend you take some time to understand the gotchas listed in the first few posts of this thread. There are limitations, for some people the limitations outweigh the advantages. Only you can determine if this extension gives you enough of what you need to warrant using it with the limitations.

