It's probably the deck cap and/or liner flexing underway, suggesting the laminate was made too thin or you have a structural issue somewhere. This isn't all that uncommon on large fixed ports or lights. Check the tabbing on roof and deck beams in the general area. Any cracks or tabbing that looks likes it's moved? I saw a large sailboat with is on all of it's oversize, stylized, quick radius corner lights (fixed window). The roof had foam beams, tabbed with a few layers of roving, some of which had delaminated. The three "beams" where replaced with Cossa and tabbed back in with biax, solving the issue.
Your current repair will hold for a while, but if there's much movement, it'll start to crack again, probably along the edges of the areas you've just repaired, at first.