It is possible I do not fully understand your set-up, but it should be quite straightforward.
Setup your course with three activities.
Activity 1: Module 1 - SCORM content 1
Activity 2: Module 2 - SCORM content 2 (Restrict Access condition = student must view Module 1)
Activity 3 = your certificate (Restrict Access condition = student must view Module 1 and Module 2)
The only problem that comes to mind, it what "completion" rule was used on the SCORM content file. All slides view = completed, number of slides = completed or a % complete grade?