I’ve got 3 Game Piece Layers in my play window
Cards
Tokens
Labels
In that order.
Cards are applied to all cards.
Tokens are markers that are placed on top of those cards.
Labels are at-start stacks that are not movable and should be drawn on top of decks. They show a count of how many cards are left in that deck.
This used to work fine before I implemented the Layers to fix an issue with saving and reloading… now, none of my Labels are visibile and they are all placed below the decks. Am I thinking of this in a completely wrong way?
Okay, I semi-figured out the problem.
Apparently, when cards are in a deck, they don’t obey the Game Piece Layers anymore.
Decks are drawn on top as if they had an empty Marker trait… which seems like a bug/missing feature. Is there a way to give a DECK a marker trait? If not… I’ll add that as a feature request. 
Yeah, cards in deck don’t obey the Game Piece Layers definition. But it was like that in Vassal 3.1.18 already, at least. Which version of Vassal are you suggesting was supporting GPL for cards in decks?
Well, I’m not sure it actually supported it or it was just a bug that made it work… but in 3.0 and 3.1, if I had the at-start stacks (with the static labels in them) BELOW the deck in the editor, they were always drawn on top of the deck. This was without using GPL at all. As soon as I turned on GPL (Which wasn’t until I updated to 3.2) they started displaying kinda random. Sometimes they would be on top, sometimes they would be below… weird stuff.
So, I eliminated them and added the piece count to the hover-zoom text.
I made some experiments back then and, if I recall correctly, items in decks will always be displayed on top. They won’t follow GPL and will want to stay top.
More precisely: you will get the random behavior you mention when looking at those decks/stacks across a network game. In other words, the synchronization process won’t guarantee any particular stacking you think you had setup (exploiting the definition order in the editor). Unless you only play on a single local computer, to guarantee the correct stacking of items across the network you better use GPL.
And then you better remember that items in deck will want to stay top no matter what.
I think I posted months ago a test module to demonstrate this (in the hope some developer would flag it as a bug and possibly fix it), but I cannot find it now. Maybe I didn’t post it after all. Will look for that test module on my other computer next time I am near it.