RE: How come the GST base amount will not show when I have input the direct cost and Line amount GST?
its difficult to troubleshoot from the information provided, but you could check the following
1/ tax area and tax jurisdiction related set up
2/ on the header and line level, if the taxable flag is set to yes
3/check if the customer, vendor, item card if any is newly set up and missing value related to tax
if there are other document which calculate correctly, compare and you might figure it out.