That's a good question. If you're using v5 of the SQLDataCompare.Engine, it checks the column collation on the first database before performing a comparison of text fields. A case-sensitive column in database1 will cause SDC to compare case-sensitively, and a case-insensitive collation will cause it to compare without regard to case.
Typically, a case-sensitive collation will have a 'CS' in the collation name, and a 'CI' if it's case-insensitive.
If the collations are both CI, then you would need to change the column in the first database to be CS. If one is CI and the other CS, you can swap the first and second databases being compared and put the case-sensitive one as the first database.
The documentation says that you can't change a field collation in code (the property is read-only).