Both JIS and ISO are square taper, they just have differing dimensions which is why a set pair of cranks will sit different distances out on each. It sounds like your cranks and BB are both JIS, which would mean that likely culprits are:
You haven't torqued the crank bolts to the right value.
The BB is installed the wrong way around
The spindle size is the wrong length.
Have you done a sanity check to make sure the spindle is the length that you meant to order?
Both JIS and ISO are square taper, they just have differing dimensions which is why a set pair of cranks will sit different distances out on each. It sounds like your cranks and BB are both JIS, which would mean that likely culprits are:
Have you done a sanity check to make sure the spindle is the length that you meant to order?