I had set-up SGST & CGST 9%(same for both) but it shows a different amount on checkout and invoice PDF. Ideally, it should be the same amount. Here are some screenshots that I have set up for GST, CGST, SGST:

As in the above image, the amounts are different

Here are tax slabs added, for GJ it’s SGST, and CGST for others it’s GST.