Thanks, Neil. It is possible, but I doubt if this is the reason in my case. I used our Build manager scripts to rebuild the application completely from scratch (bootstrapped, full built using Powergen) in PB 15. I will keep that in mind though.
One other thing that's different in our case is that ours is a n-tier application. Actual datawindow objects are all deployed in EA Server and associated with the client datawindow control at runtime using GetFullState/SetFullState functions. This may also have something to do with the issue.
I will test some more and post back the results.