The problem will be when you look at the [Financial > Charts > Open Chart of Tax Codes]. The tax will be in the right place in your Chart of Accounts, but the base and tax amounts will be missing from your Chart of Tax Codes.
A bit more detail
Each of the lines in the example (these are the Account Move Lines) can have some Tax Lines associated with them (including the Account Move Lines that are not tax amounts). These Tax Lines provide information about how much of the Account Move Line is for which tax, or how much of the Account Move Line was used as a base amount from which some tax has been calculated.
This is then used in the Chart of Tax Codes to show totals for both the tax amounts for each tax and the base amounts that the tax was applied to.
You can see a list of the Tax Lines for each Account Move Line by switching the Lines in the Account Move to form view using the [Switch] button (it’s the one with the two horizontal opposing arrows to the right of the word Lines).
So in the example, if the tax that was applied was “VAT on Purchases of Goods at Standard Rate” (called “VAT on P…” below to keep it short) then:
| Tax Lines
|-----------------------------------
Account | Tax | Amount | Type
---------------------+---------------+----------+--------
Tax Account | VAT on P... | 4.20 | Tax
Expense Account A | VAT on P... | 9.00 | Base
Expense Account B | VAT on P... | 12.00 | Base
That’s the rough idea, I’m not too sure I explained it too clearly…