VAT automated credits problems

A software company is advising agents to exercise caution when submitting their VAT returns after HMRC failed to provide automated credits where they were due in several cases.
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HMRC advice
Have you reported it? The HMRC spokesperson I talked to said people should contact the National Advice Service at the first indication of a missing payment. If it's been going on a while, perhaps you ought to ring the helpline and check the situation. In the case mentioned above, they advised that if the agent supplied registration details of the traders in question they could look into each case to determine what happened.
VAT Refunds-outstanding
For one of our Subway franchise client (new shop-fit), are due refund of atleast £35K. HMRC had witheld this reclaim, as they had not received VAT Return for April-09? No notices or reminders were sent, until we called them and found why the refunds are being witheld?
We have now, not only submitted the April-09 Return online (status was "open") but also paper Return was submitted for the same.
It has been 2 weeks now, I shall await until next week, before I pick up the phone again!!
I wander what would HMRC do, if the situation was the otherway round!!
Salil



me too
This has happened to two of my clients too - one in South Yorkshire, the other in Derbyshire! If a return was 'missing' and the next one was sent in, you would receive a reminder - they didn't.