When using the Visual Studio SQL Compare to compare your database schema to your physical database it returns heaps of false positives, where SQLCompare is suggesting that your CMD variable does not match what is on the database.
SQLCompare uses the default or local CMD variables that you have on your project when performing the compare.
You need to ensure the default variables match the target database you are comparing against.
To change your defaults open the properties of your Database project, switch to the “SQLCMD Variables” tab and edit the defaults.
When you get your variables in alignment with your target comparison database you will get a true indication of the differences.