Regarding the error message, you can try opening up the table mw_MDemand in something like Microsoft Access and look for nulls/blanks in the values in the two columns JunctionID and Sqn:
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[li]JunctionID should be the MUID for the nodes to which the demand is assigned. If there's a blank in this column, try to figure out what node the demand should be assigned to and enter its MUID. [/li]
[li]Sqn is an integer, if there are blanks here and you have more than one demand for a node, just sequentially number them (e.g., 1, 2, 3, 4, etc.). If there are blanks here and you only have one demand for each node, just enter 1 so that it's not blank anymore.[/li]
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If everything is empty in a row, it may have been added by mistake and can just be deleted.
I'm not really sure on the Scenario Manager part, it sounds like you're setting it up right. I have seen in MOUSE at least when it throws that error about the "unpredictable behavior" it gives up and doesn't actually change the scenario.