Thanks for reporting this problem.
The Compare Database Schema window compares both the unparsed procedure definition and its preserved source when determining whether two procedures are identical.
Normally, the CREATE OR REPLACE PROCEDURE statement that it generates to make the procedures match results in the identical text being inserted into the catalog for the unparsed procedure definition. However, in rare cases such as this one, the unparsed definition differs from what was specified. The procedure definitions are semantically identical, but differ slightly in semi-colon placement and white space.
While this is rare, I agree that it is not ideal. I think the solution here would be to add an option to ignore the unparsed procedure definitions if the preserved sources are identical.