V12 Item Tax Not Working (Item Tax Category and Item Tax Template)

As shown below, I am trying to set Item Tax for this particular Item but it is not working. During my creation of Sales Order, that particular item is still included in the calculation of the standard tax rate assigned in the Taxes and Charges table

We have the issue otherway round, so we got the zero VAT set up for some items and now if we make a quotation of mixed items (both with VAT 0% and VAT 24%), we get no taxes written in it.

Also, The Chart of Accounts in version 12 is showing only “Application of Funds (Assets)”. It is not showing the other branches of the Account tree, e.g. in order to make more VAT tax siblings.

I think is some problem with the Tax settings. It randomly takes any tax template even when there are tax rules defined.
Sometimes it adds the taxes twice.