Rent can be VATable - it depends on the landlord. If they decide to charge VAT, then it is reclaimable, but if they dont it obviously can't
Business Rates I am 95% sure do not attract VAT, but I could be wrong there. Business rates are paid direct to the treasury from your council so the government may have found a way of shoving the extra 17.5% on, but without checking our Business Rates bill I can't tell for sure
Well, as we're talking about a pubco here I am fairly sure they'll be VAT registered and would therefore, I think, be obliged to collect VAT.
I think that this is where the accountant is going wrong, by not claiming this VAT back. He' not a specialist Pub accountant.
It would probably be a bit daft to have business rates VATable as everyone would just claim it straight back again - unless they're not VAT registered of course.
A simple inspection of the relevant invoices will tell her whether VAT was levied or not. If she's VAT-registered, then she has to tot up all the VAT paid on her invoices, compare the figure to the sum of the VAT charged on her products/ervices to customers, and pay (or reclaim) the net difference from the VAT-man. Its not difficult - even for an accountant.