Hi @Bugsy,
At the moment Quick File only automatically handles the reverse charge on Goods and not Services, hence why the figure also appears in box 2, the guide is correct for services. You may find the posting below provides more information:
http://community.quickfile.co.uk/t/further-problems-with-vat-accounting-with-eu-suppliers/3478/3
Simply adjust out the box 2 figure on the VAT return as shown in the knowledgebase guide: