Ocasionally some orders have VAT calculated but customer has a VAT number provided

This can happen for several reasons. Please check:

• Is there any information about the validation details visible in the order comments?
  The module will let Magento calculate VAT when any of the marked results are invalid or wrong:
  
• Is the country prefix of the VAT number present at the number and does that prefix match the address (shipping) country?
  If the country information is not matching, the module will let Magento apply VAT on the order.
• For registered customers: are additional validation details saved on the customer address record (VAT is valid, VAT request success...) when you edit the customer address in the admin area?
  The validation details will be read from the address data and will be evaluated by our module to decide if Magento will apply VAT on the order.

If none of the above reasons do apply to your issue, please create a new support ticket from your customer account.