Have you introduced a new line in the procedures..?
To read from the net amount, the procedures must be set in a way.
For e.g. --
100 - BASB - Base Amount
110 - MWAS - Output Tax (calculates from base amount '100')
120 - MWVS - Input Tax (calculates from base amount '100')
130 - ZTRA - Sales Tax Withholding - (calculates from '120') from 120 to 120.
ZTRA will calculate from input tax (line 120).
OR,
Retransport the codes and Account Determination to PRD with PRD modifiable.