Proflex should always be painted so that is correct. The orange discoloration is caused by contaminants from previous sealants.
The seams should be cleaned of old sealant before applying Proflex. It may or may not work if over old sealants. Also, it's rarely the seams that leak. The edge trim (J rail, awning rail, etc) should have new putty. The wood underneath should be sound so the screws grab well and ooze the putty.