Hi Aaron,
There is a setting on your account called Assign Ref Numbers In Method? that can be found in your Method account under the Quickbooks>Synchronize tab link. If this is checked, Method will assign your reference numbers by taking the largest current number and adding one. If this is not checked, Method will wait for Quickbooks to assign the reference number upon a sync. Is this setting checked on your account?
If you activate the MethodSupport user by going to Customize>Users and checking the Active check box, I can sign in and take a look at your account. Please email me your Method Company Account name if you would like me to do so.
Jason