I am not a body man or auto finisher, but I use some of these materials in the theater stage industry and this is a technical guess.
It sounds as if the new primer is not fully bonding to the improvements you did sometime ago. Even if the body and your improvements are both 'fiberglass' the resin formulas may have been slightly different causing whatever the new primer is to not adhere equally well. As the paint dries it shrinks enough to cause the cracking where it is not immediately bonding. This effect is similar to 'faux crackling' techniques on new furniture copying antiques.
I would consider sanding off the new primer in this area and trying to reapply in multiple thin layers of spray rather than one heavy coat. You could also try a primer with a similar solvent formula from a different manufacturer. The idea here is perhaps the new 'glue' formula in the paint will be better for your situation.
If the area still cracks again, you might sand once more and try a primer with a different solvent in the formula from the ones recently applied. If you do a change up, make sure your new top coat agrees with both primers on a test sampler.