When SQL Compare compares a schema, a semantic comparison will be performed (top grid) which will group the objects based on the rules you have applied to the deployment and other basic functionally similar syntax that will automatically be ignored. It is these differences that will be deployed.
The other comparison is a straight textual comparison, that will be displayed in the bottom SQL Differences pane. All textual differences will be highlighted here. We can try match the rows as best we can, but each method will have its limitations and we don't think it would be right to reorder the SQL at this stage.
http://documentation.red-gate.com/displ ... different#
This is designed behavior and there are no plans to change the default behaviour.