Moisture is getting through the bedliner coating and entering the unsealed plywood causing it to swell, breaking the bedliner coating COhesion(coating sticking to itself)..the result is the cracking you're seeing. Once a crack appears, more moisture enters the wood and the cracking expands enough for you to see. I suspect if you took a magnifying glass and looked very closely at surfaces that appear fine to the naked eye, you'd see some cracking you haven't noticed..yet.
The bedliner appears to be moisture-permeable. If moisture gets through the liner, and that liner is sprayed on a truck-bed..no issues as the truck bed already has a exterior-durable coating on it. As long as the liner maintains ADhesion(coating sticking to the substrate) to the truck bed..all appears well. Steel doesn't absorb water, nor does it expand and contract with temp and moisture in the same order(s) of magnitude as wood does. Think microns vs millimeters.
Some thoughts::
>Spraying the bedliner, or any hopefully exterior-durable topcoat, on unfinished(unsealed) wood...not good. It's a fast, hope-for-the-best approach.
>"Sealing" the outside of unfinished wood without "sealing" the inside in the same fashion..not good. The greatest stability in wood or wood-composite panels is achieved by finishing all sides equally. Woodworkers building frame-panel cabinets or tables (or wide wall trim) always account for wood movement. Movement is limited by 6-sided finishing. The potential for wood movement in an exterior application is much greater than inside the house. Granted..wood composite panels will have much less movement than solid wood panels. When you're trying to keep exterior wood stable..I'd use every trick in the book.
>When using wood of any sort for an exterior application, I'd try to mimic the successful methods that wood-boat builders have used for decades. Particularly the stitch & glue techniques.
>I wouldn't use a thinned polyurethane to coat raw wood. It's better than nothing, but I wouldn't put a lot of faith in it. One material that boat builders, or wood-boat restoration people, use (though with some controversy), and may have good application here, is CPES (clear penetrating epoxy sealer).
Follow the directions for best results:http://www.smithandcompany.org/CPES/https://www.jamestowndistributors.com/userportal/show_product.do?pid=97636&engine=adwords!6456&keyword=cpeskw&gclid=CjwKCAiAkrTjBRAoEiwAXpf9CQAg65zYlw9e5cxv14VPanRUKkG4VYFfuTksZPCyy4SUKak6Hh0LJBoCXhQQAvD_BwEMost epoxies are not exterior (UV) durable..a topcoat would be needed.
>Any topcoat applied over the bedliner at this point assumes two things. That topcoat will adhere well to the bedliner and the bedliner will remain adhered well to the raw wood. A new topcoat can only adhere as well as what it's attached to. If you apply some coating over the bediner, at a minimum I'd rough up the surface with an orbital sander and then wipe it down with a tack-cloth (clean/disposable shop cloth and and mineral spirits wiped in one direction only)
>DON'T USE ANYTHING THAT CONTAINS SILICONE. Remove any silicone caulk you have applied with a scraper and down to the wood substrate, sand into the wood, seal it with epoxy or primer..or both.
>What to do now?
1. Fast and cheap..sand down the exterior to rough up the surface(100-125 grit), tack-cloth the dust, prime it (Glidden Gripper seems to get lots of press..I've never used it..Kilz has an exterior-grade primer-sealer), and paint it with a couple coats of premium home-siding exterior stain. (Sherwin Williams, Hallman Lindsey, Benjamin Moore). I typically go with SW products, but I used HL opaque stain on my house a couple years ago..nice stuff. If the stain sloughs off in a few years..coat it again, just like a house. Don't use anything from a box store.
2. Slower and possibly better..and more expensive..sand down the exterior to rough up the surface(100-125 grit), tack-cloth the dust, prime it (Glidden Gripper seems to get lots of press..I've never used it), and cover it with aluminum sheeting.
I'd go with option #1 and keep moving.