The problem might not have been caused by your colleague. I've seen a couple of instances where, after an upgrade, Sage's VAT settings have been a bit odd - the tax code it uses for things like transfers in particular. I don't think it was the 2009 version, though; it was more recent than that, I'm sure.
However, I don't think it should give you warnings about transactions that are T9 - but maybe it will if these settings are incorrect? Dunno...
Anyway, these instructions on what things to set are based on the 2013 version, but I think it was pretty much the same in the 2009 version:
From the menu at the top, choose Settings => Configuration. In the window that appears, click on the Tax Codes tab.
Check that the codes shown there make sense - the codes for anything that should go on the return will have a 'Y' in the 'In Use' [on a VAT return] column, so you'd expect to see a Y for the usual codes (T0 for zero rated, T1 for standard, T2 for reduced, etc) and an N for anything that won't go on the return - often T9.
You can double click on any one of them to change them.
Once you are satisfied everything is okay there...
From the menu at the top choose Settings => Company preferences In the window that appears, click on the VAT tab.
The Non-vatable tax code should be set to whichever code you use for stuff that doesn't need to go on the return - ie, the one set to 'N' for 'In Use' above; usually T9.
Hopefully, that'll put things right. (It won't change the tax codes on transfers already entered, unfortunately, but it should mean they're done correctly in future).
-- Edited by VinceH on Friday 1st of February 2013 01:39:00 PM
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Vince M Hudd - Soft Rock Software
(I only came here looking for fellow apiarists...)
My client uses Sage 50 2009 and we have 3 years of accounts on the system. I have 1638 warnings as it is saying all the bank and supplier payments are Vat code T9 which is correct but are not going into VAT return which is correct so not sure why it is alerting this warning. What is more upseting, when posting a transfer from one bank to another and also using the VAT transfer wizard, after completing Vat return, it posts these transactions automatically with a T0 code and sends the figures to the VAT account. I have checked the settings which appear to be in order. Another operator does input purchase invoices into the system wnen I am not there and I wondered if she had changed something that I am overlooking or has the programme corrupted? (Needless to say we do not pay for Sage cover so any ideas to solve the problem would be appreciated).
Excellent, I had checked the configuration settings which were OK but the Company Preferences setting for VAT had been changed from T9 to T0 and now I have amended it to show T9 the warnings have gone and the interbank transfers and VAT wizard are using T9 and NOT going into VAT. Thank you, I can now submit the VAT return correctly.