Hello Ian,
Check how far your transaction history goes back. You can specify how many days in the past you would like for your invoice to go back to. You can refer to the following post for more on transaction history: http://www.methodintegration.com/cs/forums/p/164/433.aspx#433
If the above doesn't work, then you would want to check if a full sync has been completed. You can do check this in Method by going to QuickBooks > Synchronize and check when the last Full Synchronization was performed. If it is blank then one hasn't been completed yet and you can contact your Consultant for technical support.
Let me know if that works.