Hi PwC,
I'm not sure that you should be trying to do any tax tracking in AP for those purchases originating in IC. As you noted, IC is setup to deal with the tax and between the IC Tax Tracking and GL Transactions reports you should find that it's handling these entries fine. IC generally passes a Debit to VAT Input (Paid on Purchases), Debit to Stock and a Credit to the IC/AP CLEARING accounts for Receipt transactions involving taxes to be reclaimed.
As far as AP is concerned, when it comes to posting batches passed from IC, it only needs to Debit the IC/AP CLEARING Account and Credit the appropriate AP account based on the Vendor's Account set. It doesn't really care about the tax implications since these were handled by IC already. AP however does continue to handle the Tax processing for non-IC related transactions.
Logical, but can be somewhat inconvenient from the perspective of having to refer to two separate Tax Tracking Reports to then calculate a total for submission on the Tax Returns. I have always meant to look back at this (but never got back to it) to see if there is a way to let AP do all the Tax Tracking which is what you seem to be trying to do.
So, while I offer the above as to maybe this is just how Softrak intended for it to work, I would love it to do what you want AND have all the GL entries balance.
BTW - Be careful that what you are currently doing by modifying the IC batches in AP is not actually causing problems in the GL VAT Input and IC/AP Clearing accounts. If you are truly needing to do this then something may be amiss in your IC GL integration setup.
Hope that helps, Pete
PS: I could remote in and take a look if you want. Contact me directly if this would help.