Another thought … are you expecting to see cards on those newly formed decks?
If so, that won’t happen through the Refresh. The cards will need to be placed through a separate setup routine - e.g. through a Startup GKC.
You can confirm that this is the issue by creating a brand new scenario from your module. In that case, the cards should be where you expect them to be.
I can’t recall for sure but I don’t think you even need Refresh Counters if you add a new map with decks on it. The new map will be available in the scenarios but new (i.e. “at start”) pieces/cards are never placed - not by this method, nor by Refresh Counters.