Would introducing threading help me, or am I just screwed given the scenario presented?
Absolutely! This is the exact type of thing that should be run and processed on a thread.
Also, did you guys ever discuss internally fixing the fact that DB2 tables are not properly enumerated in the BO Mapper using OLE?
Not yet. It is on our "To-do" list though. We have had some server issues recently and need to get DB2 loaded for testing.