What update are you on? 

I submitted the following to R&D and they created Bug ID# 155368 (included in APP10 UPD10): 

Bug ID# 155368: Payment VAT entries (Tax disbursed tax method -Payment) are not realized correctly for partial payment when the invoice contains WHT (withholding tax). 

In the bug record R&D stated: When correcting this bug, we noted that this is not working for different combinations that we need to deal with VAT and WHT. Therefore, having discussed with the owner, R&D decided to deliver a limited correction only. It will support only the following scenario:

WHT tax code tax method = Invoice only
VAT codes = Payment
Both customer and supplier payments will be covered.

I am not sure how you have your tax codes set up, but below is how I had mine set up for the bug:
1. Define a customer with WHT and connect WHT tax code 16% with tax disbursed tax method invoice entry.
2. Make sure you have VAT (calculated tax) code, at 16% with tax disbursed tax method payment.

If is is a different set up you should create a case, for IFS Support to recreate in core an submit to R&D..

Hi, I am currently using IFS App 10 Update 10 and App 9

in my tax code I have used

Tax Type = Tax Withhold

Tax Method Tax Received = Payment

Tax Method Tax Disbursed = Payment 

and RMB tax code > Tax withholding > use withholding amount table (Ticked)

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Sorry for the late response, but I think you need to create a Support Case and have someone in Support test this in core.  I used a Sales Tax Company, not Mixed. I used 2 tax codes on my order:  

1. WHT tax code
2.  Calculated tax code (Vat)

R&D only fixed my specific set-up with Bug ID# 155368.  So I think you should log a case with IFS Support and have them test in core. It could very well be a bug.