Its quite common for the guitars with the same style
neck joint as the JS. A lot of older RG's have neck joint finish cracks too.
So long as it is just a finish crack then i wouldnt worry. My EBMM JP has a small (around 1cm) crack in the top of the neck pocket. Its just because that area of the neck has a decent amount of pressure on it, and if the corners are sharp, then it can cause the
clear coat to crack.
Im sure Rich will spot this thread and explain it better

. He mentioned that the new Ibanez cases arent helping the JS's when it comes to NJFCs wither.