I notified QBO about this 2 years ago and several times since. They are well aware of the problem and have done nothing..Ian R ShawRegency Organics Ltd.
I have been in touch with quickbooks regarding this problem many times over the past 2 years and always get the same reply " Their engineers are working on it "...
Yes, we use the flat rate scheme although we no longer do our VAT return through QBO due to errors with the purchase of reverse charge services from the EU.