Fees (in fact all costs) can only be collected to the lowest unit of currency, which is 1p.
I think eBay rounds fees up or down to the nearest full penny. Certainly when sellers have underpaid by enough part-pence to make a full penny, this is added to their next invoice. We sometimes get questions about the additional penny!
I'm guessing that with VAT eBay always rounds it up, as they can't get away with paying VAT even a fraction of a penny short! Whether eBay keeps the remaining part-penny in your account, I don't know!
Somebody more familiar with VAT may know how its dealt with.
