Hi there, thanks for posting.
If the tables in question don't have any kind of key or unique index on them, you need to specify one (our engine needs to have *something* to compare on, else it doesn't know what should match up and what shouldn't).
Assuming you can determine a column (or combination of columns) that will uniquely identify rows in some way, then you can tell the tool to use this. In the GUI, it's a case of selecting the columns by going to the Tables & Views tab, then clicking in the first column for the given table.
In the SDK, you can do the same thing through the "MatchingMappings" collection. Have a look at the "TableMappingExample" in the SQLDataCompareSnippets example that's installed with the SDK for example usage.