If you don't use merge, and what you are doing instead is loading into a single table multiple times in the same data flow, you may run into issues. Again this is using MS SQL Server, but you can run into deadlocks if you try and insert into the same table at the same time. It is also possible the reason your data flow doesn't work is whatever database you are using locks the table and gets stuck in a similar way. If you have access to a DBA, they should be able to tell you if this is the case.
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