I am able to reproduce the problem in both EG 7.12 HF9 and EG 7.15. As you mentioned, I do think it is related to having the same source table in both process flows. I'll enter it into our tracking system, so we can hopefully address in a future release.
In the meantime, I was able to workaround by selecting only the program node (ex. "Code For sdf") and moving it by itself or by copy/pasting just the program to the desired process flow.
Sorry for the inconvenience.
Casey
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