shoebox with ninja 90cub in tank

Either the gauge is wrong and your regulator is not working, or you have some bad disc's. On a 90CI Ninja tank the output side which is the 5K disc should see 3K max no matter what is in the tank.
You don't have 5K disc on the main disc do you? This one should be a 7.5K disc.
Also make sure the "pocket" where the disc's go does not have anything in it. These disc's are meant to be "flat" against the bottom of the hole. If something is causing the disc to not fully seat then this could be causing it to rupture.