We also meet same problem “Missing AgreementID” as well. It’s glad to hear that this problem been resolved by your own. Might I know where you changed the Join Type? (Ex. which step in WM:Modeler??)
Really, really , really hope that more information that I can try to solved this problme in our B2B system (WM 6.1)… 
Thank you for your cooperatin in advanced. 
#webMethods#Adapters-and-E-Standards#Integration-Server-and-ESB