Time to start thinking laterally - you said you have two stoves set up with similar flue etc, one burns good, one doesn't . Next time they are both cold, switch the front doors over. Also, I can't remember on the Bubble how it lets air in, because if you are not getting good controlled air in it will burn badly. Check the air in vents are clear. Worth a try anyway!
You may be getting close to calling in an expert - if the engineer from Lockgate Stoves will work on a Bubble I can highly recommend him. Not cheap but as Red Adair once said 'if you think a professional is expensive, wait till you hire an amateur'.