UK Cis tax and VAT in wrong order

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Hi,

I'm a CIS and VAT registered subcontractor. I have recently finished a few weeks work for a contractor I have previously not worked for.
I sent my invoice in and it was duly paid by BACS but the amount paid was short of the invoice value and I had no payment certificate from the contractor to explain the differences.
After a few weeks asking for a payment cert one has finally arrived and the reason for the confusion is because the contractor is ignoring my final VAT value but instead calculating the VAT after deducting 20% CIS.

I have not yet contacted the contractor but my main question is who is liable to pay the shortfall in VAT to HMRC?
So what would happen if nothing was done, would it eventually come out in the wash once all the accounts had been done an would I be liable for it even though I have never actually received it? Surely the VAT man will want it but from whom?
It has taken me nearly 4 weeks to get a poxy payment certificate from them so god knows how long it will take to get them to pay the VAT shortfall which amounts to approx £350
 

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